@gmod/cram - npm Package Compare versions

Comparing version 1.5.9 to 1.6.0

dist/craiIndex.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _sort = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/sort"));
-
-var _entries = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/entries"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _parseInt = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/number/parse-int"));
-
-var _bind = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/bind"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/slicedToArray"));
-
-var _some = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/some"));
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _assign = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/assign"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var AbortablePromiseCache = require('abortable-promise-cache').default;
-
-var QuickLRU = require('quick-lru');
-
-var _require = require('es6-promisify'),
-    promisify = _require.promisify;
-
-var zlib = require('zlib');
-
-var gunzip = promisify(zlib.gunzip);
-
-var _require2 = require('./io'),
-    open = _require2.open;
-
-var _require3 = require('./errors'),
-    CramMalformedError = _require3.CramMalformedError;
-
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
+var quick_lru_1 = __importDefault(require("quick-lru"));
+var es6_promisify_1 = require("es6-promisify");
+var zlib_1 = __importDefault(require("zlib"));
+var io_1 = require("./io");
+var errors_1 = require("./errors");
+var gunzip = (0, es6_promisify_1.promisify)(zlib_1.default.gunzip);
 var BAI_MAGIC = 21578050; // BAI\1
-
-var Slice =
-/*#__PURE__*/
-function () {
-  function Slice(args) {
-    (0, _classCallCheck2.default)(this, Slice);
-    (0, _assign.default)(this, args);
-  }
-
-  (0, _createClass2.default)(Slice, [{
-    key: "toString",
-    value: function toString() {
-      var _context, _context2, _context3, _context4;
-
-      return (0, _concat.default)(_context = (0, _concat.default)(_context2 = (0, _concat.default)(_context3 = (0, _concat.default)(_context4 = "".concat(this.start, ":")).call(_context4, this.span, ":")).call(_context3, this.containerStart, ":")).call(_context2, this.sliceStart, ":")).call(_context, this.sliceBytes);
+var Slice = /** @class */ (function () {
+    function Slice(args) {
+        Object.assign(this, args);
     }
-  }]);
-  return Slice;
-}();
-
+    Slice.prototype.toString = function () {
+        return "".concat(this.start, ":").concat(this.span, ":").concat(this.containerStart, ":").concat(this.sliceStart, ":").concat(this.sliceBytes);
+    };
+    return Slice;
+}());
 function addRecordToIndex(index, record) {
-  if ((0, _some.default)(record).call(record, function (el) {
-    return el === undefined;
-  })) {
-    throw new CramMalformedError('invalid .crai index file');
-  }
-
-  var _record = (0, _slicedToArray2.default)(record, 6),
-      seqId = _record[0],
-      start = _record[1],
-      span = _record[2],
-      containerStart = _record[3],
-      sliceStart = _record[4],
-      sliceBytes = _record[5];
-
-  if (!index[seqId]) index[seqId] = [];
-  index[seqId].push(new Slice({
-    start: start,
-    span: span,
-    containerStart: containerStart,
-    sliceStart: sliceStart,
-    sliceBytes: sliceBytes
-  }));
+    if (record.some(function (el) { return el === undefined; })) {
+        throw new errors_1.CramMalformedError('invalid .crai index file');
+    }
+    var seqId = record[0], start = record[1], span = record[2], containerStart = record[3], sliceStart = record[4], sliceBytes = record[5];
+    if (!index[seqId]) {
+        index[seqId] = [];
+    }
+    index[seqId].push(new Slice({
+        start: start,
+        span: span,
+        containerStart: containerStart,
+        sliceStart: sliceStart,
+        sliceBytes: sliceBytes,
+    }));
 }
-
-var CraiIndex =
-/*#__PURE__*/
-function () {
-  // 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]
-   */
-  function CraiIndex(args) {
-    var _this = this,
-        _context5;
-
-    (0, _classCallCheck2.default)(this, CraiIndex);
-    var filehandle = open(args.url, args.path, args.filehandle);
-    this._parseCache = new AbortablePromiseCache({
-      cache: new QuickLRU({
-        maxSize: 1
-      }),
-      fill: function fill(data, signal) {
-        return _this.parseIndex({
-          signal: signal
+var CraiIndex = /** @class */ (function () {
+    // 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]
+     */
+    function CraiIndex(args) {
+        var _this = this;
+        var 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: function (data, signal) { return _this.parseIndex({ signal: signal }); },
         });
-      }
-    });
-    this.readFile = (0, _bind.default)(_context5 = filehandle.readFile).call(_context5, filehandle);
-  }
-
-  (0, _createClass2.default)(CraiIndex, [{
-    key: "parseIndex",
-    value: function parseIndex() {
-      var index = {};
-      return this.readFile().then(function (data) {
-        if (data[0] === 31 && data[1] === 139) return gunzip(data);
-        return data;
-      }).then(function (uncompressedBuffer) {
-        var _context6;
-
-        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.
-
-
-        var currentRecord = [];
-        var currentString = '';
-
-        for (var i = 0; i < uncompressedBuffer.length; i += 1) {
-          var 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((0, _parseInt.default)(currentString, 10));
-              currentString = '';
-            } else if (charCode === 10
-          /* \n */
-          ) {
-              currentRecord.push((0, _parseInt.default)(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');
+        this.readFile = filehandle.readFile.bind(filehandle);
+    }
+    CraiIndex.prototype.parseIndex = function () {
+        var index = {};
+        return this.readFile()
+            .then(function (data) {
+            if (data[0] === 31 && data[1] === 139) {
+                return gunzip(data);
             }
-        } // if the file ends without a \n, we need to flush our buffers
-
-
-        if (currentString) {
-          currentRecord.push((0, _parseInt.default)(currentString, 10));
-        }
-
-        if (currentRecord.length === 6) {
-          addRecordToIndex(index, currentRecord);
-        } // sort each of them by start
-
-
-        (0, _forEach.default)(_context6 = (0, _entries.default)(index)).call(_context6, function (_ref) {
-          var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-              seqId = _ref2[0],
-              ent = _ref2[1];
-
-          index[seqId] = (0, _sort.default)(ent).call(ent, function (a, b) {
-            return a.start - b.start || a.span - b.span;
-          });
+            return data;
+        })
+            .then(function (uncompressedBuffer) {
+            if (uncompressedBuffer.length > 4 &&
+                uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC) {
+                throw new errors_1.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.
+            var currentRecord = [];
+            var currentString = '';
+            for (var i = 0; i < uncompressedBuffer.length; i += 1) {
+                var 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 errors_1.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(function (_a) {
+                var seqId = _a[0], ent = _a[1];
+                index[seqId] = ent.sort(function (a, b) { return a.start - b.start || a.span - b.span; });
+            });
+            return index;
         });
-        return index;
-      });
-    }
-  }, {
-    key: "getIndex",
-    value: function getIndex() {
-      var opts = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-      return this._parseCache.get('index', null, opts.signal);
-    }
+    };
+    CraiIndex.prototype.getIndex = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return this._parseCache.get('index', null, opts.signal);
+    };
     /**
@@ -218,34 +166,12 @@ * @param {number} seqId
      */
-
-  }, {
-    key: "hasDataForReferenceSequence",
-    value: function () {
-      var _hasDataForReferenceSequence = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee(seqId) {
-        return _regenerator.default.wrap(function _callee$(_context7) {
-          while (1) {
-            switch (_context7.prev = _context7.next) {
-              case 0:
-                _context7.next = 2;
-                return this.getIndex();
-
-              case 2:
-                _context7.t0 = seqId;
-                return _context7.abrupt("return", !!_context7.sent[_context7.t0]);
-
-              case 4:
-              case "end":
-                return _context7.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function hasDataForReferenceSequence(_x) {
-        return _hasDataForReferenceSequence.apply(this, arguments);
-      }
-
-      return hasDataForReferenceSequence;
-    }()
+    CraiIndex.prototype.hasDataForReferenceSequence = function (seqId) {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getIndex()];
+                    case 1: return [2 /*return*/, !!(_a.sent())[seqId]];
+                }
+            });
+        });
+    };
     /**
@@ -262,67 +188,38 @@ * fetch index entries for the given range
      */
-
-  }, {
-    key: "getEntriesForRange",
-    value: function () {
-      var _getEntriesForRange = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee2(seqId, queryStart, queryEnd) {
-        var seqEntries, compare, bins, i;
-        return _regenerator.default.wrap(function _callee2$(_context8) {
-          while (1) {
-            switch (_context8.prev = _context8.next) {
-              case 0:
-                _context8.next = 2;
-                return this.getIndex();
-
-              case 2:
-                _context8.t0 = seqId;
-                seqEntries = _context8.sent[_context8.t0];
-
-                if (seqEntries) {
-                  _context8.next = 6;
-                  break;
+    CraiIndex.prototype.getEntriesForRange = function (seqId, queryStart, queryEnd) {
+        return __awaiter(this, void 0, void 0, function () {
+            var seqEntries, compare, bins, i;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getIndex()];
+                    case 1:
+                        seqEntries = (_a.sent())[seqId];
+                        if (!seqEntries) {
+                            return [2 /*return*/, []];
+                        }
+                        compare = function (entry) {
+                            var entryStart = entry.start;
+                            var 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
+                        };
+                        bins = [];
+                        for (i = 0; i < seqEntries.length; i += 1) {
+                            if (compare(seqEntries[i]) === 0) {
+                                bins.push(seqEntries[i]);
+                            }
+                        }
+                        return [2 /*return*/, bins];
                 }
-
-                return _context8.abrupt("return", []);
-
-              case 6:
-                compare = function compare(entry) {
-                  var entryStart = entry.start;
-                  var 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
-                };
-
-                bins = [];
-
-                for (i = 0; i < seqEntries.length; i += 1) {
-                  if (compare(seqEntries[i]) === 0) {
-                    bins.push(seqEntries[i]);
-                  }
-                }
-
-                return _context8.abrupt("return", bins);
-
-              case 10:
-              case "end":
-                return _context8.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getEntriesForRange(_x2, _x3, _x4) {
-        return _getEntriesForRange.apply(this, arguments);
-      }
-
-      return getEntriesForRange;
-    }()
-  }]);
-  return CraiIndex;
-}();
-
-module.exports = CraiIndex;
+            });
+        });
+    };
+    return CraiIndex;
+}());
+exports.default = CraiIndex;
+//# sourceMappingURL=craiIndex.js.map

dist/cramFile/codecs/_base.js

 "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

dist/cramFile/codecs/beta.js

 "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

dist/cramFile/codecs/byteArrayLength.js

 "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

dist/cramFile/codecs/byteArrayStop.js

 "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));
+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));
+        }
+        return _this;
     }
-
-    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?");
+    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));
         }
-
-        stopPosition += 1;
-      }
-
-      cursor.bytePosition = stopPosition + 1;
-      var data = (0, _slice.default)(dataBuffer).call(dataBuffer, startPosition, stopPosition);
-      return data;
-    }
-  }]);
-  return ByteArrayStopCodec;
-}(CramCodec);
-
-module.exports = ByteArrayStopCodec;
+        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

dist/cramFile/codecs/external.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/slicedToArray"));
-
-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,
-    CramMalformedError = _require.CramMalformedError,
-    CramBufferOverrunError = _require.CramBufferOverrunError;
-
-var CramCodec = require('./_base');
-
-var _require2 = require('../util'),
-    parseItf8 = _require2.parseItf8;
-
-var ExternalCodec =
-/*#__PURE__*/
-function (_CramCodec) {
-  (0, _inherits2.default)(ExternalCodec, _CramCodec);
-
-  function ExternalCodec() {
-    var _this;
-
-    var parameters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-    var dataType = arguments.length > 1 ? arguments[1] : undefined;
-    (0, _classCallCheck2.default)(this, ExternalCodec);
-    _this = (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(ExternalCodec).call(this, parameters, dataType));
-
-    if (_this.dataType === 'int') {
-      _this._decodeData = _this._decodeInt;
-    } else if (_this.dataType === 'byte') {
-      _this._decodeData = _this._decodeByte;
-    } else {
-      throw new CramUnimplementedError("".concat(_this.dataType, " decoding not yet implemented by EXTERNAL 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 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;
+        }
+        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"));
+        }
+        return _this;
     }
-
-    return _this;
-  }
-
-  (0, _createClass2.default)(ExternalCodec, [{
-    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._decodeData(contentBlock, cursor);
-    }
-  }, {
-    key: "_decodeInt",
-    value: function _decodeInt(contentBlock, cursor) {
-      var _parseItf = parseItf8(contentBlock.content, cursor.bytePosition),
-          _parseItf2 = (0, _slicedToArray2.default)(_parseItf, 2),
-          result = _parseItf2[0],
-          bytesRead = _parseItf2[1];
-
-      cursor.bytePosition += bytesRead;
-      return result;
-    }
-  }, {
-    key: "_decodeByte",
-    value: function _decodeByte(contentBlock, cursor) {
-      if (cursor.bytePosition >= contentBlock.content.length) throw new CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
-      var result = contentBlock.content[cursor.bytePosition];
-      cursor.bytePosition += 1;
-      return result;
-    }
-  }]);
-  return ExternalCodec;
-}(CramCodec);
-
-module.exports = ExternalCodec;
+    ExternalCodec.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._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;
+        return result;
+    };
+    ExternalCodec.prototype._decodeByte = function (contentBlock, cursor) {
+        if (cursor.bytePosition >= contentBlock.content.length) {
+            throw new errors_1.CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
+        }
+        var result = contentBlock.content[cursor.bytePosition];
+        cursor.bytePosition += 1;
+        return result;
+    };
+    return ExternalCodec;
+}(_base_1.default));
+exports.default = ExternalCodec;
+//# sourceMappingURL=external.js.map

dist/cramFile/codecs/gamma.js

 "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 GammaCodec =
-/*#__PURE__*/
-function (_CramCodec) {
-  (0, _inherits2.default)(GammaCodec, _CramCodec);
-
-  function GammaCodec() {
-    var _this;
-
-    var parameters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-    var dataType = arguments.length > 1 ? arguments[1] : undefined;
-    (0, _classCallCheck2.default)(this, GammaCodec);
-    _this = (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(GammaCodec).call(this, parameters, dataType));
-
-    if (_this.dataType !== 'int') {
-      throw new CramUnimplementedError("".concat(_this.dataType, " decoding not yet implemented by GAMMA 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 GammaCodec = /** @class */ (function (_super) {
+    __extends(GammaCodec, _super);
+    function GammaCodec(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 GAMMA codec"));
+        }
+        return _this;
     }
-
-    return _this;
-  }
-
-  (0, _createClass2.default)(GammaCodec, [{
-    key: "decode",
-    value: function decode(slice, coreDataBlock, blocksByContentId, cursors) {
-      var length = 1;
-
-      while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
-        length += 1;
-      }
-
-      var readBits = this._getBits(coreDataBlock.content, cursors.coreBlock, length - 1);
-
-      var value = readBits | 1 << length - 1;
-      return value - this.parameters.offset;
-    }
-  }]);
-  return GammaCodec;
-}(CramCodec);
-
-module.exports = GammaCodec;
+    GammaCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
+        var length = 1;
+        while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
+            length += 1;
+        }
+        var readBits = this._getBits(coreDataBlock.content, cursors.coreBlock, length - 1);
+        var value = readBits | (1 << (length - 1));
+        return value - this.parameters.offset;
+    };
+    return GammaCodec;
+}(_base_1.default));
+exports.default = GammaCodec;
+//# sourceMappingURL=gamma.js.map

dist/cramFile/codecs/huffman.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _fill = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/fill"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/toConsumableArray"));
-
-var _map = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/map"));
-
-var _values = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/values"));
-
-var _parseInt2 = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/parse-int"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/slicedToArray"));
-
-var _entries = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/entries"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _sort = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/sort"));
-
-var _includes = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/includes"));
-
-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'),
-    CramMalformedError = _require.CramMalformedError;
-
-var CramCodec = require('./_base');
-
+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"));
 function numberOfSetBits(ii) {
-  var i = ii - (ii >> 1) & 0x55555555;
-  i = (i & 0x33333333) + (i >> 2 & 0x33333333);
-  return (i + (i >> 4) & 0x0f0f0f0f) * 0x01010101 >> 24;
+    var i = (ii - (ii >> 1)) & 0x55555555;
+    i = (i & 0x33333333) + ((i >> 2) & 0x33333333);
+    return (((i + (i >> 4)) & 0x0f0f0f0f) * 0x01010101) >> 24;
 }
-
-var HuffmanIntCodec =
-/*#__PURE__*/
-function (_CramCodec) {
-  (0, _inherits2.default)(HuffmanIntCodec, _CramCodec);
-
-  function HuffmanIntCodec() {
-    var _context;
-
-    var _this;
-
-    var parameters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-    var dataType = arguments.length > 1 ? arguments[1] : undefined;
-    (0, _classCallCheck2.default)(this, HuffmanIntCodec);
-    _this = (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(HuffmanIntCodec).call(this, parameters, dataType));
-
-    if (!(0, _includes.default)(_context = ['byte', 'int']).call(_context, _this.dataType)) {
-      throw new TypeError("".concat(_this.dataType, " decoding not yet implemented by HUFFMAN_INT codec"));
+var HuffmanIntCodec = /** @class */ (function (_super) {
+    __extends(HuffmanIntCodec, _super);
+    function HuffmanIntCodec(parameters, dataType) {
+        if (parameters === void 0) { parameters = {}; }
+        var _this = _super.call(this, parameters, dataType) || this;
+        if (!['byte', 'int'].includes(_this.dataType)) {
+            throw new TypeError("".concat(_this.dataType, " decoding not yet implemented by HUFFMAN_INT codec"));
+        }
+        _this.buildCodeBook();
+        _this.buildCodes();
+        _this.buildCaches();
+        // if this is a degenerate zero-length huffman code, special-case the decoding
+        if (_this.sortedCodes[0].bitLength === 0) {
+            _this._decode = _this._decodeZeroLengthCode;
+        }
+        return _this;
     }
-
-    _this.buildCodeBook();
-
-    _this.buildCodes();
-
-    _this.buildCaches(); // if this is a degenerate zero-length huffman code, special-case the decoding
-
-
-    if (_this.sortedCodes[0].bitLength === 0) _this._decode = _this._decodeZeroLengthCode;
-    return _this;
-  }
-
-  (0, _createClass2.default)(HuffmanIntCodec, [{
-    key: "buildCodeBook",
-    value: function buildCodeBook() {
-      var _this2 = this;
-
-      // parse the parameters together into a `codes` data structure
-      var codes = new Array(this.parameters.numCodes);
-
-      for (var i = 0; i < this.parameters.numCodes; i += 1) {
-        codes[i] = {
-          symbol: this.parameters.symbols[i],
-          bitLength: this.parameters.bitLengths[i]
-        };
-      } // sort the codes by bit length and symbol value
-
-
-      codes = (0, _sort.default)(codes).call(codes, function (a, b) {
-        return a.bitLength - b.bitLength || a.symbol - b.symbol;
-      });
-      this.codeBook = {};
-      (0, _forEach.default)(codes).call(codes, function (code) {
-        if (!_this2.codeBook[code.bitLength]) _this2.codeBook[code.bitLength] = [];
-
-        _this2.codeBook[code.bitLength].push(code.symbol);
-      });
-    }
-  }, {
-    key: "buildCodes",
-    value: function buildCodes() {
-      var _context2,
-          _this3 = this;
-
-      this.codes = {};
-      /*  new TreeMap<Integer, HuffmanBitCode>(); */
-
-      var codeLength = 0;
-      var codeValue = -1;
-      (0, _forEach.default)(_context2 = (0, _entries.default)(this.codeBook)).call(_context2, function (_ref) {
-        var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-            bitLength = _ref2[0],
-            symbols = _ref2[1];
-
-        bitLength = (0, _parseInt2.default)(bitLength, 10);
-        (0, _forEach.default)(symbols).call(symbols, function (symbol) {
-          var code = {
-            bitLength: bitLength,
-            value: symbol
-          };
-          codeValue += 1;
-          var delta = bitLength - codeLength; // new length?
-
-          codeValue <<= delta; // pad with 0's
-
-          code.bitCode = codeValue; // calculated: huffman code
-
-          codeLength += delta; // adjust current code length
-
-          if (numberOfSetBits(codeValue) > bitLength) throw new CramMalformedError('Symbol out of range');
-          _this3.codes[symbol] = code;
+    HuffmanIntCodec.prototype.buildCodeBook = function () {
+        var _this = this;
+        // parse the parameters together into a `codes` data structure
+        var codes = new Array(this.parameters.numCodes);
+        for (var i = 0; i < this.parameters.numCodes; i += 1) {
+            codes[i] = {
+                symbol: this.parameters.symbols[i],
+                bitLength: this.parameters.bitLengths[i],
+            };
+        }
+        // sort the codes by bit length and symbol value
+        codes = codes.sort(function (a, b) { return a.bitLength - b.bitLength || a.symbol - b.symbol; });
+        this.codeBook = {};
+        codes.forEach(function (code) {
+            if (!_this.codeBook[code.bitLength]) {
+                _this.codeBook[code.bitLength] = [];
+            }
+            _this.codeBook[code.bitLength].push(code.symbol);
         });
-      });
-    }
-  }, {
-    key: "buildCaches",
-    value: function buildCaches() {
-      var _context3, _context4, _context5, _context6, _context7, _context8;
-
-      this.sortedCodes = (0, _sort.default)(_context3 = (0, _values.default)(this.codes)).call(_context3, function (a, b) {
-        return a.bitLength - b.bitLength || a.bitCode - b.bitCode;
-      }); // this.sortedValues = this.parameters.values.sort((a,b) => a-b)
-
-      this.sortedByValue = (0, _sort.default)(_context4 = (0, _values.default)(this.codes)).call(_context4, function (a, b) {
-        return a.value - b.value;
-      });
-      this.sortedValuesByBitCode = (0, _map.default)(_context5 = this.sortedCodes).call(_context5, function (c) {
-        return c.value;
-      });
-      this.sortedBitCodes = (0, _map.default)(_context6 = this.sortedCodes).call(_context6, function (c) {
-        return c.bitCode;
-      });
-      this.sortedBitLengthsByBitCode = (0, _map.default)(_context7 = this.sortedCodes).call(_context7, function (c) {
-        return c.bitLength;
-      });
-      var maxBitCode = Math.max.apply(Math, (0, _toConsumableArray2.default)(this.sortedBitCodes));
-      this.bitCodeToValue = (0, _fill.default)(_context8 = new Array(maxBitCode + 1)).call(_context8, -1);
-
-      for (var i = 0; i < this.sortedBitCodes.length; i += 1) {
-        this.bitCodeToValue[this.sortedCodes[i].bitCode] = i;
-      }
-    }
-  }, {
-    key: "decode",
-    value: function decode(slice, coreDataBlock, blocksByContentId, cursors) {
-      return this._decode(slice, coreDataBlock, cursors.coreBlock);
-    } // _decodeNull() {
+    };
+    HuffmanIntCodec.prototype.buildCodes = function () {
+        var _this = this;
+        this.codes = {}; /*  new TreeMap<Integer, HuffmanBitCode>(); */
+        var codeLength = 0;
+        var codeValue = -1;
+        Object.entries(this.codeBook).forEach(function (_a) {
+            var bitLength = _a[0], symbols = _a[1];
+            bitLength = parseInt(bitLength, 10);
+            symbols.forEach(function (symbol) {
+                var code = { bitLength: bitLength, value: symbol };
+                codeValue += 1;
+                var delta = bitLength - codeLength; // new length?
+                codeValue <<= delta; // pad with 0's
+                code.bitCode = codeValue; // calculated: huffman code
+                codeLength += delta; // adjust current code length
+                if (numberOfSetBits(codeValue) > bitLength) {
+                    throw new errors_1.CramMalformedError('Symbol out of range');
+                }
+                _this.codes[symbol] = code;
+            });
+        });
+    };
+    HuffmanIntCodec.prototype.buildCaches = function () {
+        this.sortedCodes = Object.values(this.codes).sort(function (a, b) { return a.bitLength - b.bitLength || a.bitCode - b.bitCode; });
+        // this.sortedValues = this.parameters.values.sort((a,b) => a-b)
+        this.sortedByValue = Object.values(this.codes).sort(function (a, b) { return a.value - b.value; });
+        this.sortedValuesByBitCode = this.sortedCodes.map(function (c) { return c.value; });
+        this.sortedBitCodes = this.sortedCodes.map(function (c) { return c.bitCode; });
+        this.sortedBitLengthsByBitCode = this.sortedCodes.map(function (c) { return c.bitLength; });
+        var maxBitCode = Math.max.apply(Math, this.sortedBitCodes);
+        this.bitCodeToValue = new Array(maxBitCode + 1).fill(-1);
+        for (var i = 0; i < this.sortedBitCodes.length; i += 1) {
+            this.bitCodeToValue[this.sortedCodes[i].bitCode] = i;
+        }
+    };
+    HuffmanIntCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
+        return this._decode(slice, coreDataBlock, cursors.coreBlock);
+    };
+    // _decodeNull() {
     //   return -1
     // }
     // the special case for zero-length codes
-
-  }, {
-    key: "_decodeZeroLengthCode",
-    value: function _decodeZeroLengthCode() {
-      return this.sortedCodes[0].value;
-    }
-  }, {
-    key: "_decode",
-    value: function _decode(slice, coreDataBlock, coreCursor) {
-      var input = coreDataBlock.content;
-      var prevLen = 0;
-      var bits = 0;
-
-      for (var i = 0; i < this.sortedCodes.length; i += 1) {
-        var length = this.sortedCodes[i].bitLength;
-        bits <<= length - prevLen;
-        bits |= this._getBits(input, coreCursor, length - prevLen);
-        prevLen = length;
-        {
-          var index = this.bitCodeToValue[bits];
-          if (index > -1 && this.sortedBitLengthsByBitCode[index] === length) return this.sortedValuesByBitCode[index];
-
-          for (var j = i; this.sortedCodes[j + 1].bitLength === length && j < this.sortedCodes.length; j += 1) {
-            i += 1;
-          }
+    HuffmanIntCodec.prototype._decodeZeroLengthCode = function () {
+        return this.sortedCodes[0].value;
+    };
+    HuffmanIntCodec.prototype._decode = function (slice, coreDataBlock, coreCursor) {
+        var input = coreDataBlock.content;
+        var prevLen = 0;
+        var bits = 0;
+        for (var i = 0; i < this.sortedCodes.length; i += 1) {
+            var length_1 = this.sortedCodes[i].bitLength;
+            bits <<= length_1 - prevLen;
+            bits |= this._getBits(input, coreCursor, length_1 - prevLen);
+            prevLen = length_1;
+            {
+                var index = this.bitCodeToValue[bits];
+                if (index > -1 && this.sortedBitLengthsByBitCode[index] === length_1) {
+                    return this.sortedValuesByBitCode[index];
+                }
+                for (var j = i; this.sortedCodes[j + 1].bitLength === length_1 &&
+                    j < this.sortedCodes.length; j += 1) {
+                    i += 1;
+                }
+            }
         }
-      }
-
-      throw new CramMalformedError('Huffman symbol not found.');
-    }
-  }]);
-  return HuffmanIntCodec;
-}(CramCodec);
-
-module.exports = HuffmanIntCodec;
+        throw new errors_1.CramMalformedError('Huffman symbol not found.');
+    };
+    return HuffmanIntCodec;
+}(_base_1.default));
+exports.default = HuffmanIntCodec;
+//# sourceMappingURL=huffman.js.map

dist/cramFile/codecs/index.js

 "use strict";
-
-var _require = require('../../errors'),
-    CramUnimplementedError = _require.CramUnimplementedError;
-
-var HuffmanIntCodec = require('./huffman');
-
-var ExternalCodec = require('./external');
-
-var ByteArrayStopCodec = require('./byteArrayStop');
-
-var ByteArrayLengthCodec = require('./byteArrayLength');
-
-var BetaCodec = require('./beta');
-
-var GammaCodec = require('./gamma');
-
-var SubexpCodec = require('./subexp');
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.instantiateCodec = exports.getCodecClassWithId = void 0;
+var errors_1 = require("../../errors");
+var huffman_1 = __importDefault(require("./huffman"));
+var external_1 = __importDefault(require("./external"));
+var byteArrayStop_1 = __importDefault(require("./byteArrayStop"));
+var byteArrayLength_1 = __importDefault(require("./byteArrayLength"));
+var beta_1 = __importDefault(require("./beta"));
+var gamma_1 = __importDefault(require("./gamma"));
+var subexp_1 = __importDefault(require("./subexp"));
 var codecClasses = {
-  1: ExternalCodec,
-  // 2: GolombCodec,
-  3: HuffmanIntCodec,
-  4: ByteArrayLengthCodec,
-  5: ByteArrayStopCodec,
-  6: BetaCodec,
-  7: SubexpCodec,
-  // 8: GolombRiceCodec,
-  9: GammaCodec
+    1: external_1.default,
+    // 2: GolombCodec,
+    3: huffman_1.default,
+    4: byteArrayLength_1.default,
+    5: byteArrayStop_1.default,
+    6: beta_1.default,
+    7: subexp_1.default,
+    // 8: GolombRiceCodec,
+    9: gamma_1.default,
 };
-
 function getCodecClassWithId(id) {
-  return codecClasses[id];
+    return codecClasses[id];
 }
-
+exports.getCodecClassWithId = getCodecClassWithId;
 function instantiateCodec(encodingData, dataType) {
-  var CodecClass = getCodecClassWithId(dataType === 'ignore' ? 0 : encodingData.codecId);
-  if (!CodecClass) throw new CramUnimplementedError("no codec implemented for codec ID ".concat(encodingData.codecId));
-  return new CodecClass(encodingData.parameters, dataType, instantiateCodec);
+    var CodecClass = getCodecClassWithId(dataType === 'ignore' ? 0 : encodingData.codecId);
+    if (!CodecClass) {
+        throw new errors_1.CramUnimplementedError("no codec implemented for codec ID ".concat(encodingData.codecId));
+    }
+    return new CodecClass(encodingData.parameters, dataType, instantiateCodec);
 }
-
-module.exports = {
-  getCodecClassWithId: getCodecClassWithId,
-  instantiateCodec: instantiateCodec
-};
+exports.instantiateCodec = instantiateCodec;
+//# sourceMappingURL=index.js.map

dist/cramFile/codecs/subexp.js

 "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 SubexpCodec =
-/*#__PURE__*/
-function (_CramCodec) {
-  (0, _inherits2.default)(SubexpCodec, _CramCodec);
-
-  function SubexpCodec() {
-    var _this;
-
-    var parameters = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-    var dataType = arguments.length > 1 ? arguments[1] : undefined;
-    (0, _classCallCheck2.default)(this, SubexpCodec);
-    _this = (0, _possibleConstructorReturn2.default)(this, (0, _getPrototypeOf2.default)(SubexpCodec).call(this, parameters, dataType));
-
-    if (_this.dataType !== 'int') {
-      throw new CramUnimplementedError("".concat(_this.dataType, " decoding not yet implemented by SUBEXP 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 SubexpCodec = /** @class */ (function (_super) {
+    __extends(SubexpCodec, _super);
+    function SubexpCodec(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 SUBEXP codec"));
+        }
+        return _this;
     }
-
-    return _this;
-  }
-
-  (0, _createClass2.default)(SubexpCodec, [{
-    key: "decode",
-    value: function decode(slice, coreDataBlock, blocksByContentId, cursors) {
-      var numLeadingOnes = 0;
-
-      while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
-        numLeadingOnes += 1;
-      }
-
-      var b;
-      var n;
-
-      if (numLeadingOnes === 0) {
-        b = this.parameters.K;
-        n = this._getBits(coreDataBlock.content, cursors.coreBlock, b);
-      } else {
-        b = numLeadingOnes + this.parameters.K - 1;
-        n = 1 << b | this._getBits(coreDataBlock.content, cursors.coreBlock, b);
-      }
-
-      return n - this.parameters.offset;
-    }
-  }]);
-  return SubexpCodec;
-}(CramCodec);
-
-module.exports = SubexpCodec;
+    SubexpCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
+        var numLeadingOnes = 0;
+        while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
+            numLeadingOnes += 1;
+        }
+        var b;
+        var n;
+        if (numLeadingOnes === 0) {
+            b = this.parameters.K;
+            n = this._getBits(coreDataBlock.content, cursors.coreBlock, b);
+        }
+        else {
+            b = numLeadingOnes + this.parameters.K - 1;
+            n = (1 << b) | this._getBits(coreDataBlock.content, cursors.coreBlock, b);
+        }
+        return n - this.parameters.offset;
+    };
+    return SubexpCodec;
+}(_base_1.default));
+exports.default = SubexpCodec;
+//# sourceMappingURL=subexp.js.map

dist/cramFile/constants.js

 "use strict";
-
-module.exports = {
-  CRAM_FLAG_PRESERVE_QUAL_SCORES: 1 << 0,
-  CRAM_FLAG_DETACHED: 1 << 1,
-  CRAM_FLAG_MATE_DOWNSTREAM: 1 << 2,
-  CRAM_FLAG_NO_SEQ: 1 << 3,
-  CRAM_FLAG_MASK: (1 << 4) - 1,
-  // mate read is reversed
-  CRAM_M_REVERSE: 1,
-  // mated read is unmapped
-  CRAM_M_UNMAP: 2,
-  //  the read is paired in sequencing, no matter whether it is mapped in a pair
-  BAM_FPAIRED: 1,
-  //  the read is mapped in a proper pair
-  BAM_FPROPER_PAIR: 2,
-  //  the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
-  BAM_FUNMAP: 4,
-  //  the mate is unmapped
-  BAM_FMUNMAP: 8,
-  //  the read is mapped to the reverse strand
-  BAM_FREVERSE: 16,
-  //  the mate is mapped to the reverse strand
-  BAM_FMREVERSE: 32,
-  //  this is read1
-  BAM_FREAD1: 64,
-  //  this is read2
-  BAM_FREAD2: 128,
-  //  not primary alignment
-  BAM_FSECONDARY: 256,
-  //  QC failure
-  BAM_FQCFAIL: 512,
-  //  optical or PCR duplicate
-  BAM_FDUP: 1024,
-  //  supplementary alignment
-  BAM_FSUPPLEMENTARY: 2048,
-  BAM_CMATCH: 0,
-  BAM_CINS: 1,
-  BAM_CDEL: 2,
-  BAM_CREF_SKIP: 3,
-  BAM_CSOFT_CLIP: 4,
-  BAM_CHARD_CLIP: 5,
-  BAM_CPAD: 6,
-  BAM_CEQUAL: 7,
-  BAM_CDIFF: 8,
-  BAM_CBACK: 9,
-  BAM_CIGAR_STR: 'MIDNSHP:XB',
-  BAM_CIGAR_SHIFT: 4,
-  BAM_CIGAR_MASK: 0xf,
-  BAM_CIGAR_TYPE: 0x3c1a7
-};
+Object.defineProperty(exports, "__esModule", { value: true });
+var Constants = {
+    CRAM_FLAG_PRESERVE_QUAL_SCORES: 1 << 0,
+    CRAM_FLAG_DETACHED: 1 << 1,
+    CRAM_FLAG_MATE_DOWNSTREAM: 1 << 2,
+    CRAM_FLAG_NO_SEQ: 1 << 3,
+    CRAM_FLAG_MASK: (1 << 4) - 1,
+    // mate read is reversed
+    CRAM_M_REVERSE: 1,
+    // mated read is unmapped
+    CRAM_M_UNMAP: 2,
+    //  the read is paired in sequencing, no matter whether it is mapped in a pair
+    BAM_FPAIRED: 1,
+    //  the read is mapped in a proper pair
+    BAM_FPROPER_PAIR: 2,
+    //  the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
+    BAM_FUNMAP: 4,
+    //  the mate is unmapped
+    BAM_FMUNMAP: 8,
+    //  the read is mapped to the reverse strand
+    BAM_FREVERSE: 16,
+    //  the mate is mapped to the reverse strand
+    BAM_FMREVERSE: 32,
+    //  this is read1
+    BAM_FREAD1: 64,
+    //  this is read2
+    BAM_FREAD2: 128,
+    //  not primary alignment
+    BAM_FSECONDARY: 256,
+    //  QC failure
+    BAM_FQCFAIL: 512,
+    //  optical or PCR duplicate
+    BAM_FDUP: 1024,
+    //  supplementary alignment
+    BAM_FSUPPLEMENTARY: 2048,
+    BAM_CMATCH: 0,
+    BAM_CINS: 1,
+    BAM_CDEL: 2,
+    BAM_CREF_SKIP: 3,
+    BAM_CSOFT_CLIP: 4,
+    BAM_CHARD_CLIP: 5,
+    BAM_CPAD: 6,
+    BAM_CEQUAL: 7,
+    BAM_CDIFF: 8,
+    BAM_CBACK: 9,
+    BAM_CIGAR_STR: 'MIDNSHP:XB',
+    BAM_CIGAR_SHIFT: 4,
+    BAM_CIGAR_MASK: 0xf,
+    BAM_CIGAR_TYPE: 0x3c1a7,
+};
+exports.default = Constants;
+//# sourceMappingURL=constants.js.map

dist/cramFile/container/compressionScheme.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _keys = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/keys"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _assign = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/assign"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _require = require('../../errors'),
-    CramMalformedError = _require.CramMalformedError;
-
-var _require2 = require('../codecs'),
-    instantiateCodec = _require2.instantiateCodec; // the hardcoded data type to be decoded for each core
+Object.defineProperty(exports, "__esModule", { value: true });
+var errors_1 = require("../../errors");
+var codecs_1 = require("../codecs");
+// the hardcoded data type to be decoded for each core
 // data field
-
-
 var dataSeriesTypes = {
-  BF: 'int',
-  CF: 'int',
-  RI: 'int',
-  RL: 'int',
-  AP: 'int',
-  RG: 'int',
-  MF: 'int',
-  NS: 'int',
-  NP: 'int',
-  TS: 'int',
-  NF: 'int',
-  TC: 'byte',
-  TN: 'int',
-  FN: 'int',
-  FC: 'byte',
-  FP: 'int',
-  BS: 'byte',
-  IN: 'byteArray',
-  SC: 'byteArray',
-  DL: 'int',
-  BA: 'byte',
-  BB: 'byteArray',
-  RS: 'int',
-  PD: 'int',
-  HC: 'int',
-  MQ: 'int',
-  RN: 'byteArray',
-  QS: 'byte',
-  QQ: 'byteArray',
-  TL: 'int',
-  TM: 'ignore',
-  TV: 'ignore'
+    BF: 'int',
+    CF: 'int',
+    RI: 'int',
+    RL: 'int',
+    AP: 'int',
+    RG: 'int',
+    MF: 'int',
+    NS: 'int',
+    NP: 'int',
+    TS: 'int',
+    NF: 'int',
+    TC: 'byte',
+    TN: 'int',
+    FN: 'int',
+    FC: 'byte',
+    FP: 'int',
+    BS: 'byte',
+    IN: 'byteArray',
+    SC: 'byteArray',
+    DL: 'int',
+    BA: 'byte',
+    BB: 'byteArray',
+    RS: 'int',
+    PD: 'int',
+    HC: 'int',
+    MQ: 'int',
+    RN: 'byteArray',
+    QS: 'byte',
+    QQ: 'byteArray',
+    TL: 'int',
+    TM: 'ignore',
+    TV: 'ignore',
 };
-
 function parseSubstitutionMatrix(byteArray) {
-  var matrix = new Array(5);
-
-  for (var i = 0; i < 5; i += 1) {
-    matrix[i] = new Array(4);
-  }
-
-  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[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[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';
-  return matrix;
+    var matrix = new Array(5);
+    for (var i = 0; i < 5; i += 1) {
+        matrix[i] = new Array(4);
+    }
+    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[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[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';
+    return matrix;
 }
-
-var CramContainerCompressionScheme =
-/*#__PURE__*/
-function () {
-  function CramContainerCompressionScheme(content) {
-    (0, _classCallCheck2.default)(this, CramContainerCompressionScheme);
-    (0, _assign.default)(this, content); // interpret some of the preservation map tags for convenient use
-
-    this.readNamesIncluded = content.preservation.RN;
-    this.APdelta = content.preservation.AP;
-    this.referenceRequired = !!content.preservation.RR;
-    this.tagIdsDictionary = content.preservation.TD;
-    this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
-    this.dataSeriesCodecCache = {};
-    this.tagCodecCache = {};
-  }
-  /**
-   * @param {string} tagName three-character tag name
-   * @private
-   */
-
-
-  (0, _createClass2.default)(CramContainerCompressionScheme, [{
-    key: "getCodecForTag",
-    value: function getCodecForTag(tagName) {
-      if (!this.tagCodecCache[tagName]) {
-        var encodingData = this.tagEncoding[tagName];
-
-        if (encodingData) {
-          this.tagCodecCache[tagName] = instantiateCodec(encodingData, 'byteArray' // all tags are byte array data
-          );
-        }
-      }
-
-      return this.tagCodecCache[tagName];
+var CramContainerCompressionScheme = /** @class */ (function () {
+    function CramContainerCompressionScheme(content) {
+        Object.assign(this, content);
+        // interpret some of the preservation map tags for convenient use
+        this.readNamesIncluded = content.preservation.RN;
+        this.APdelta = content.preservation.AP;
+        this.referenceRequired = !!content.preservation.RR;
+        this.tagIdsDictionary = content.preservation.TD;
+        this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
+        this.dataSeriesCodecCache = {};
+        this.tagCodecCache = {};
     }
     /**
+     * @param {string} tagName three-character tag name
+     * @private
+     */
+    CramContainerCompressionScheme.prototype.getCodecForTag = function (tagName) {
+        if (!this.tagCodecCache[tagName]) {
+            var encodingData = this.tagEncoding[tagName];
+            if (encodingData) {
+                this.tagCodecCache[tagName] = (0, codecs_1.instantiateCodec)(encodingData, 'byteArray');
+            }
+        }
+        return this.tagCodecCache[tagName];
+    };
+    /**
      *
@@ -128,40 +98,32 @@ * @param {number} tagListId ID of the tag list to fetch from the tag dictionary
      */
-
-  }, {
-    key: "getTagNames",
-    value: function getTagNames(tagListId) {
-      return this.tagIdsDictionary[tagListId];
-    }
-  }, {
-    key: "getCodecForDataSeries",
-    value: function getCodecForDataSeries(dataSeriesName) {
-      if (!this.dataSeriesCodecCache[dataSeriesName]) {
-        var encodingData = this.dataSeriesEncoding[dataSeriesName];
-
-        if (encodingData) {
-          var dataType = dataSeriesTypes[dataSeriesName];
-          if (!dataType) throw new CramMalformedError("data series name ".concat(dataSeriesName, " not defined in file compression header"));
-          this.dataSeriesCodecCache[dataSeriesName] = instantiateCodec(encodingData, dataType);
+    CramContainerCompressionScheme.prototype.getTagNames = function (tagListId) {
+        return this.tagIdsDictionary[tagListId];
+    };
+    CramContainerCompressionScheme.prototype.getCodecForDataSeries = function (dataSeriesName) {
+        if (!this.dataSeriesCodecCache[dataSeriesName]) {
+            var encodingData = this.dataSeriesEncoding[dataSeriesName];
+            if (encodingData) {
+                var dataType = dataSeriesTypes[dataSeriesName];
+                if (!dataType) {
+                    throw new errors_1.CramMalformedError("data series name ".concat(dataSeriesName, " not defined in file compression header"));
+                }
+                this.dataSeriesCodecCache[dataSeriesName] = (0, codecs_1.instantiateCodec)(encodingData, dataType);
+            }
         }
-      }
-
-      return this.dataSeriesCodecCache[dataSeriesName];
-    }
-  }, {
-    key: "toJSON",
-    value: function toJSON() {
-      var _context,
-          _this = this;
-
-      var data = {};
-      (0, _forEach.default)(_context = (0, _keys.default)(this)).call(_context, function (k) {
-        if (/Cache$/.test(k)) return;
-        data[k] = _this[k];
-      });
-      return data;
-    }
-  }]);
-  return CramContainerCompressionScheme;
-}();
-
-module.exports = CramContainerCompressionScheme;
+        return this.dataSeriesCodecCache[dataSeriesName];
+    };
+    CramContainerCompressionScheme.prototype.toJSON = function () {
+        var _this = this;
+        var data = {};
+        Object.keys(this).forEach(function (k) {
+            if (/Cache$/.test(k)) {
+                return;
+            }
+            data[k] = _this[k];
+        });
+        return data;
+    };
+    return CramContainerCompressionScheme;
+}());
+exports.default = CramContainerCompressionScheme;
+//# sourceMappingURL=compressionScheme.js.map

dist/cramFile/container/index.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _assign = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/assign"));
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _context7;
-
-var _require = require('../../errors'),
-    CramMalformedError = _require.CramMalformedError;
-
-var _require2 = require('../util'),
-    itf8Size = _require2.itf8Size,
-    parseItem = _require2.parseItem,
-    tinyMemoize = _require2.tinyMemoize;
-
-var CramSlice = require('../slice');
-
-var CramContainerCompressionScheme = require('./compressionScheme');
-
-var CramContainer =
-/*#__PURE__*/
-function () {
-  function CramContainer(cramFile, position) {
-    (0, _classCallCheck2.default)(this, CramContainer);
-    // cram file this container comes from
-    this.file = cramFile; // position of this container in the file
-
-    this.filePosition = position; // console.log(`container: ${this.filePosition}`)
-  } // memoize
-
-
-  (0, _createClass2.default)(CramContainer, [{
-    key: "getHeader",
-    value: function getHeader() {
-      return this._readContainerHeader(this.filePosition);
-    } // memoize
-
-  }, {
-    key: "getCompressionHeaderBlock",
-    value: function () {
-      var _getCompressionHeaderBlock = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee() {
-        var containerHeader, sectionParsers, block, content;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.getHeader();
-
-              case 2:
-                containerHeader = _context.sent;
-
-                if (containerHeader.numRecords) {
-                  _context.next = 5;
-                  break;
-                }
-
-                return _context.abrupt("return", null);
-
-              case 5:
-                _context.next = 7;
-                return this.file.getSectionParsers();
-
-              case 7:
-                sectionParsers = _context.sent;
-                _context.next = 10;
-                return this.getFirstBlock();
-
-              case 10:
-                block = _context.sent;
-
-                if (!(block.contentType !== 'COMPRESSION_HEADER')) {
-                  _context.next = 13;
-                  break;
-                }
-
-                throw new CramMalformedError("invalid content type ".concat(block.contentType, " in what is supposed to be the compression header block"));
-
-              case 13:
-                content = parseItem(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
-                block.content = content;
-                return _context.abrupt("return", block);
-
-              case 16:
-              case "end":
-                return _context.stop();
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
             }
-          }
-        }, _callee, this);
-      }));
-
-      function getCompressionHeaderBlock() {
-        return _getCompressionHeaderBlock.apply(this, arguments);
-      }
-
-      return getCompressionHeaderBlock;
-    }()
-  }, {
-    key: "getFirstBlock",
-    value: function () {
-      var _getFirstBlock = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee2() {
-        var containerHeader;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.getHeader();
-
-              case 2:
-                containerHeader = _context2.sent;
-                return _context2.abrupt("return", this.file.readBlock(containerHeader._endPosition));
-
-              case 4:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getFirstBlock() {
-        return _getFirstBlock.apply(this, arguments);
-      }
-
-      return getFirstBlock;
-    }() // parses the compression header data into a CramContainerCompressionScheme object
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+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 util_1 = require("../util");
+var slice_1 = __importDefault(require("../slice"));
+var compressionScheme_1 = __importDefault(require("./compressionScheme"));
+var CramContainer = /** @class */ (function () {
+    function CramContainer(cramFile, position) {
+        // cram file this container comes from
+        this.file = cramFile;
+        // position of this container in the file
+        this.filePosition = position;
+        // console.log(`container: ${this.filePosition}`)
+    }
     // memoize
-
-  }, {
-    key: "getCompressionScheme",
-    value: function () {
-      var _getCompressionScheme = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee3() {
-        var header;
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return this.getCompressionHeaderBlock();
-
-              case 2:
-                header = _context3.sent;
-
-                if (header) {
-                  _context3.next = 5;
-                  break;
+    CramContainer.prototype.getHeader = function () {
+        return this._readContainerHeader(this.filePosition);
+    };
+    // memoize
+    CramContainer.prototype.getCompressionHeaderBlock = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var containerHeader, sectionParsers, block, content;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getHeader()
+                        // if there are no records in the container, there will be no compression header
+                    ];
+                    case 1:
+                        containerHeader = _a.sent();
+                        // if there are no records in the container, there will be no compression header
+                        if (!containerHeader.numRecords) {
+                            return [2 /*return*/, null];
+                        }
+                        return [4 /*yield*/, this.file.getSectionParsers()];
+                    case 2:
+                        sectionParsers = _a.sent();
+                        return [4 /*yield*/, this.getFirstBlock()];
+                    case 3:
+                        block = _a.sent();
+                        if (block.contentType !== 'COMPRESSION_HEADER') {
+                            throw new errors_1.CramMalformedError("invalid content type ".concat(block.contentType, " in what is supposed to be the compression header block"));
+                        }
+                        content = (0, util_1.parseItem)(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
+                        block.content = content;
+                        return [2 /*return*/, block];
                 }
-
-                return _context3.abrupt("return", undefined);
-
-              case 5:
-                return _context3.abrupt("return", new CramContainerCompressionScheme(header.content));
-
-              case 6:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getCompressionScheme() {
-        return _getCompressionScheme.apply(this, arguments);
-      }
-
-      return getCompressionScheme;
-    }()
-  }, {
-    key: "getSlice",
-    value: function getSlice(slicePosition, sliceSize) {
-      // note: slicePosition is relative to the end of the container header
-      // TODO: perhaps we should cache slices?
-      return new CramSlice(this, slicePosition, sliceSize);
-    }
-  }, {
-    key: "_readContainerHeader",
-    value: function () {
-      var _readContainerHeader2 = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee4(position) {
-        var sectionParsers, cramContainerHeader1, cramContainerHeader2, _ref, fileSize, bytes1, header1, numLandmarksSize, _context4, _context5, bytes2, header2, completeHeader;
-
-        return _regenerator.default.wrap(function _callee4$(_context6) {
-          while (1) {
-            switch (_context6.prev = _context6.next) {
-              case 0:
-                _context6.next = 2;
-                return this.file.getSectionParsers();
-
-              case 2:
-                sectionParsers = _context6.sent;
-                cramContainerHeader1 = sectionParsers.cramContainerHeader1, cramContainerHeader2 = sectionParsers.cramContainerHeader2;
-                _context6.next = 6;
-                return this.file.stat();
-
-              case 6:
-                _ref = _context6.sent;
-                fileSize = _ref.size;
-
-                if (!(position >= fileSize)) {
-                  _context6.next = 10;
-                  break;
+            });
+        });
+    };
+    CramContainer.prototype.getFirstBlock = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var containerHeader;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getHeader()];
+                    case 1:
+                        containerHeader = _a.sent();
+                        return [2 /*return*/, this.file.readBlock(containerHeader._endPosition)];
                 }
-
-                return _context6.abrupt("return", undefined);
-
-              case 10:
-                // parse the container header. do it in 2 pieces because you cannot tell
-                // how much to buffer until you read numLandmarks
-                bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength);
-                _context6.next = 13;
-                return this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position);
-
-              case 13:
-                header1 = parseItem(bytes1, cramContainerHeader1.parser);
-                numLandmarksSize = itf8Size(header1.numLandmarks);
-
-                if (!(position + header1.length >= fileSize)) {
-                  _context6.next = 18;
-                  break;
+            });
+        });
+    };
+    // parses the compression header data into a CramContainerCompressionScheme object
+    // memoize
+    CramContainer.prototype.getCompressionScheme = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var header;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getCompressionHeaderBlock()];
+                    case 1:
+                        header = _a.sent();
+                        if (!header) {
+                            return [2 /*return*/, undefined];
+                        }
+                        return [2 /*return*/, new compressionScheme_1.default(header.content)];
                 }
-
-                console.warn((0, _concat.default)(_context4 = (0, _concat.default)(_context5 = "".concat(this.file, ": container header at ")).call(_context5, position, " indicates that the container has length ")).call(_context4, header1.length, ", which extends beyond the length of the file. Skipping this container."));
-                return _context6.abrupt("return", undefined);
-
-              case 18:
-                bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
-                _context6.next = 21;
-                return this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
-
-              case 21:
-                header2 = parseItem(bytes2, cramContainerHeader2.parser);
-
-                if (!(this.file.validateChecksums && header2.crc32 !== undefined)) {
-                  _context6.next = 25;
-                  break;
+            });
+        });
+    };
+    CramContainer.prototype.getSlice = function (slicePosition, sliceSize) {
+        // note: slicePosition is relative to the end of the container header
+        // TODO: perhaps we should cache slices?
+        return new slice_1.default(this, slicePosition, sliceSize);
+    };
+    CramContainer.prototype._readContainerHeader = function (position) {
+        return __awaiter(this, void 0, void 0, function () {
+            var sectionParsers, cramContainerHeader1, cramContainerHeader2, fileSize, bytes1, header1, numLandmarksSize, bytes2, header2, completeHeader;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.file.getSectionParsers()];
+                    case 1:
+                        sectionParsers = _a.sent();
+                        cramContainerHeader1 = sectionParsers.cramContainerHeader1, cramContainerHeader2 = sectionParsers.cramContainerHeader2;
+                        return [4 /*yield*/, this.file.stat()];
+                    case 2:
+                        fileSize = (_a.sent()).size;
+                        if (position >= fileSize) {
+                            return [2 /*return*/, undefined];
+                        }
+                        bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength);
+                        return [4 /*yield*/, this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position)];
+                    case 3:
+                        _a.sent();
+                        header1 = (0, util_1.parseItem)(bytes1, cramContainerHeader1.parser);
+                        numLandmarksSize = (0, util_1.itf8Size)(header1.numLandmarks);
+                        if (position + header1.length >= fileSize) {
+                            console.warn("".concat(this.file, ": container header at ").concat(position, " indicates that the container has length ").concat(header1.length, ", which extends beyond the length of the file. Skipping this container."));
+                            return [2 /*return*/, undefined];
+                        }
+                        bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
+                        return [4 /*yield*/, this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize)];
+                    case 4:
+                        _a.sent();
+                        header2 = (0, util_1.parseItem)(bytes2, cramContainerHeader2.parser);
+                        if (!(this.file.validateChecksums && header2.crc32 !== undefined)) return [3 /*break*/, 6];
+                        return [4 /*yield*/, this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, "container header beginning at position ".concat(position))];
+                    case 5:
+                        _a.sent();
+                        _a.label = 6;
+                    case 6:
+                        completeHeader = Object.assign(header1, header2, {
+                            _size: header1._size + header2._size - numLandmarksSize,
+                            _endPosition: header1._size + header2._size - numLandmarksSize + position,
+                        });
+                        return [2 /*return*/, completeHeader];
                 }
-
-                _context6.next = 25;
-                return this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, "container header beginning at position ".concat(position));
-
-              case 25:
-                completeHeader = (0, _assign.default)(header1, header2, {
-                  _size: header1._size + header2._size - numLandmarksSize,
-                  _endPosition: header1._size + header2._size - numLandmarksSize + position
-                });
-                return _context6.abrupt("return", completeHeader);
-
-              case 27:
-              case "end":
-                return _context6.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function _readContainerHeader(_x) {
-        return _readContainerHeader2.apply(this, arguments);
-      }
-
-      return _readContainerHeader;
-    }()
-  }]);
-  return CramContainer;
-}();
-
-(0, _forEach.default)(_context7 = 'getHeader getCompressionHeaderBlock getCompressionScheme'.split(' ')).call(_context7, function (method) {
-  return tinyMemoize(CramContainer, method);
-});
-module.exports = CramContainer;
+            });
+        });
+    };
+    return CramContainer;
+}());
+exports.default = CramContainer;
+'getHeader getCompressionHeaderBlock getCompressionScheme'
+    .split(' ')
+    .forEach(function (method) { return (0, util_1.tinyMemoize)(CramContainer, method); });
+//# sourceMappingURL=index.js.map

dist/cramFile/file.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _context14;
-
-var zlib = require('zlib');
-
-var crc32 = require('buffer-crc32');
-
-var LRU = require('quick-lru');
-
-var _require = require('../errors'),
-    CramUnimplementedError = _require.CramUnimplementedError,
-    CramMalformedError = _require.CramMalformedError;
-
-var rans = require('../rans');
-
-var _require2 = require('./sectionParsers'),
-    cramFileDefinitionParser = _require2.cramFileDefinition,
-    _getSectionParsers = _require2.getSectionParsers;
-
-var CramContainer = require('./container');
-
-var _require3 = require('../io'),
-    open = _require3.open;
-
-var _require4 = require('./util'),
-    parseItem = _require4.parseItem,
-    tinyMemoize = _require4.tinyMemoize;
-
-var _require5 = require('../sam'),
-    parseHeaderText = _require5.parseHeaderText;
-
-var CramFile =
-/*#__PURE__*/
-function () {
-  /**
-   * @param {object} args
-   * @param {object} [args.filehandle] - a filehandle that implements the stat() and
-   * read() methods of the Node filehandle API https://nodejs.org/api/fs.html#fs_class_filehandle
-   * @param {object} [args.path] - path to the cram file
-   * @param {object} [args.url] - url for the cram file.  also supports file:// urls for local files
-   * @param {function} [args.seqFetch] - a function with signature
-   * `(seqId, startCoordinate, endCoordinate)` that returns a promise for a string of sequence bases
-   * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
-   * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
-   * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
-   */
-  function CramFile(args) {
-    (0, _classCallCheck2.default)(this, CramFile);
-    this.file = open(args.url, args.path, args.filehandle);
-    this.validateChecksums = true;
-    this.fetchReferenceSequenceCallback = args.seqFetch;
-    this.options = {
-      checkSequenceMD5: args.checkSequenceMD5 !== false,
-      cacheSize: args.cacheSize !== undefined ? args.cacheSize : 20000
-    }; // 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 LRU({
-      maxSize: this.options.cacheSize
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
-  }
-
-  (0, _createClass2.default)(CramFile, [{
-    key: "toString",
-    value: function toString() {
-      if (this.file.filename) return this.file.filename;
-      if (this.file.url) return this.file.url;
-      return '(cram file)';
-    } // can just read this object like a filehandle
-
-  }, {
-    key: "read",
-    value: function read(buffer, offset, length, position) {
-      return this.file.read(buffer, offset, length, position);
-    } // can just stat this object like a filehandle
-
-  }, {
-    key: "stat",
-    value: function stat() {
-      return this.file.stat();
-    } // memoized
-
-  }, {
-    key: "getDefinition",
-    value: function () {
-      var _getDefinition = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee() {
-        var headbytes, definition;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                headbytes = Buffer.allocUnsafe(cramFileDefinitionParser.maxLength);
-                _context.next = 3;
-                return this.file.read(headbytes, 0, cramFileDefinitionParser.maxLength, 0);
-
-              case 3:
-                definition = cramFileDefinitionParser.parser.parse(headbytes).result;
-
-                if (!(definition.majorVersion !== 2 && definition.majorVersion !== 3)) {
-                  _context.next = 6;
-                  break;
-                }
-
-                throw new CramUnimplementedError("CRAM version ".concat(definition.majorVersion, " not supported"));
-
-              case 6:
-                return _context.abrupt("return", definition);
-
-              case 7:
-              case "end":
-                return _context.stop();
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
             }
-          }
-        }, _callee, this);
-      }));
-
-      function getDefinition() {
-        return _getDefinition.apply(this, arguments);
-      }
-
-      return getDefinition;
-    }() // memoize
-
-  }, {
-    key: "getSamHeader",
-    value: function () {
-      var _getSamHeader = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee2() {
-        var firstContainer, _ref, content, headerLength, textStart, text;
-
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.getContainerById(0);
-
-              case 2:
-                firstContainer = _context2.sent;
-
-                if (firstContainer) {
-                  _context2.next = 5;
-                  break;
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var zlib_1 = __importDefault(require("zlib"));
+var buffer_crc32_1 = __importDefault(require("buffer-crc32"));
+var quick_lru_1 = __importDefault(require("quick-lru"));
+var errors_1 = require("../errors");
+var rans_1 = __importDefault(require("../rans"));
+var sectionParsers_1 = require("./sectionParsers");
+var htscodecs_1 = __importDefault(require("@jkbonfield/htscodecs"));
+var container_1 = __importDefault(require("./container"));
+var io_1 = require("../io");
+var util_1 = require("./util");
+var sam_1 = require("../sam");
+var CramFile = /** @class */ (function () {
+    /**
+     * @param {object} args
+     * @param {object} [args.filehandle] - a filehandle that implements the stat() and
+     * read() methods of the Node filehandle API https://nodejs.org/api/fs.html#fs_class_filehandle
+     * @param {object} [args.path] - path to the cram file
+     * @param {object} [args.url] - url for the cram file.  also supports file:// urls for local files
+     * @param {function} [args.seqFetch] - a function with signature
+     * `(seqId, startCoordinate, endCoordinate)` that returns a promise for a string of sequence bases
+     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
+     * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
+     * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
+     */
+    function CramFile(args) {
+        this.file = (0, io_1.open)(args.url, args.path, args.filehandle);
+        this.validateChecksums = true;
+        this.fetchReferenceSequenceCallback = args.seqFetch;
+        this.options = {
+            checkSequenceMD5: args.checkSequenceMD5 !== false,
+            cacheSize: args.cacheSize !== undefined ? args.cacheSize : 20000,
+        };
+        // 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({
+            maxSize: this.options.cacheSize,
+        });
+    }
+    CramFile.prototype.toString = function () {
+        if (this.file.filename) {
+            return this.file.filename;
+        }
+        if (this.file.url) {
+            return this.file.url;
+        }
+        return '(cram file)';
+    };
+    // can just read this object like a filehandle
+    CramFile.prototype.read = function (buffer, offset, length, position) {
+        return this.file.read(buffer, offset, length, position);
+    };
+    // can just stat this object like a filehandle
+    CramFile.prototype.stat = function () {
+        return this.file.stat();
+    };
+    // memoized
+    CramFile.prototype.getDefinition = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var headbytes, definition;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        headbytes = Buffer.allocUnsafe(sectionParsers_1.cramFileDefinition.maxLength);
+                        return [4 /*yield*/, this.file.read(headbytes, 0, sectionParsers_1.cramFileDefinition.maxLength, 0)];
+                    case 1:
+                        _a.sent();
+                        definition = sectionParsers_1.cramFileDefinition.parser.parse(headbytes).result;
+                        if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
+                            throw new errors_1.CramUnimplementedError("CRAM version ".concat(definition.majorVersion, " not supported"));
+                        }
+                        return [2 /*return*/, definition];
                 }
-
-                throw new CramMalformedError('file contains no containers');
-
-              case 5:
-                _context2.next = 7;
-                return firstContainer.getFirstBlock();
-
-              case 7:
-                _ref = _context2.sent;
-                content = _ref.content;
-                // find the end of the trailing zeros in the header text
-                headerLength = content.readInt32LE(0);
-                textStart = 4; // let textEnd = content.length - 1
-                // while (textEnd >= textStart && !content[textEnd]) textEnd -= 1
-                // trim off the trailing zeros
-
-                text = content.toString('utf8', textStart, textStart + headerLength);
-                this.header = text;
-                return _context2.abrupt("return", parseHeaderText(text));
-
-              case 14:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getSamHeader() {
-        return _getSamHeader.apply(this, arguments);
-      }
-
-      return getSamHeader;
-    }()
-  }, {
-    key: "getHeaderText",
-    value: function () {
-      var _getHeaderText = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee3() {
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return this.getSamHeader();
-
-              case 2:
-                return _context3.abrupt("return", this.header);
-
-              case 3:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getHeaderText() {
-        return _getHeaderText.apply(this, arguments);
-      }
-
-      return getHeaderText;
-    }() // memoize
-
-  }, {
-    key: "getSectionParsers",
-    value: function () {
-      var _getSectionParsers2 = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee4() {
-        var _ref2, majorVersion;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.getDefinition();
-
-              case 2:
-                _ref2 = _context4.sent;
-                majorVersion = _ref2.majorVersion;
-                return _context4.abrupt("return", _getSectionParsers(majorVersion));
-
-              case 5:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function getSectionParsers() {
-        return _getSectionParsers2.apply(this, arguments);
-      }
-
-      return getSectionParsers;
-    }()
-  }, {
-    key: "getContainerById",
-    value: function () {
-      var _getContainerById = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee5(containerNumber) {
-        var sectionParsers, position, _ref3, fileSize, cramContainerHeader1, currentContainer, i, currentHeader, j, block;
-
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
-                _context5.next = 2;
-                return this.getSectionParsers();
-
-              case 2:
-                sectionParsers = _context5.sent;
-                position = sectionParsers.cramFileDefinition.maxLength;
-                _context5.next = 6;
-                return this.file.stat();
-
-              case 6:
-                _ref3 = _context5.sent;
-                fileSize = _ref3.size;
-                cramContainerHeader1 = sectionParsers.cramContainerHeader1; // skip with a series of reads to the proper container
-
-                i = 0;
-
-              case 10:
-                if (!(i <= containerNumber)) {
-                  _context5.next = 36;
-                  break;
+            });
+        });
+    };
+    // memoize
+    CramFile.prototype.getSamHeader = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var firstContainer, content, headerLength, textStart, text;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getContainerById(0)];
+                    case 1:
+                        firstContainer = _a.sent();
+                        if (!firstContainer) {
+                            throw new errors_1.CramMalformedError('file contains no containers');
+                        }
+                        return [4 /*yield*/, firstContainer.getFirstBlock()
+                            // find the end of the trailing zeros in the header text
+                        ];
+                    case 2:
+                        content = (_a.sent()).content;
+                        headerLength = content.readInt32LE(0);
+                        textStart = 4;
+                        text = content.toString('utf8', textStart, textStart + headerLength);
+                        this.header = text;
+                        return [2 /*return*/, (0, sam_1.parseHeaderText)(text)];
                 }
-
-                if (!(position + cramContainerHeader1.maxLength + 8 >= fileSize)) {
-                  _context5.next = 13;
-                  break;
+            });
+        });
+    };
+    CramFile.prototype.getHeaderText = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getSamHeader()];
+                    case 1:
+                        _a.sent();
+                        return [2 /*return*/, this.header];
                 }
-
-                return _context5.abrupt("return", undefined);
-
-              case 13:
-                currentContainer = this.getContainerAtPosition(position);
-                _context5.next = 16;
-                return currentContainer.getHeader();
-
-              case 16:
-                currentHeader = _context5.sent;
-
-                if (currentHeader) {
-                  _context5.next = 19;
-                  break;
+            });
+        });
+    };
+    // memoize
+    CramFile.prototype.getSectionParsers = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var majorVersion;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getDefinition()];
+                    case 1:
+                        majorVersion = (_a.sent()).majorVersion;
+                        return [2 /*return*/, (0, sectionParsers_1.getSectionParsers)(majorVersion)];
                 }
-
-                throw new CramMalformedError("container ".concat(containerNumber, " not found in file"));
-
-              case 19:
-                if (!(i === 0)) {
-                  _context5.next = 32;
-                  break;
+            });
+        });
+    };
+    CramFile.prototype.getContainerById = function (containerNumber) {
+        return __awaiter(this, void 0, void 0, function () {
+            var sectionParsers, position, fileSize, cramContainerHeader1, currentContainer, i, currentHeader, j, block;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getSectionParsers()];
+                    case 1:
+                        sectionParsers = _a.sent();
+                        position = sectionParsers.cramFileDefinition.maxLength;
+                        return [4 /*yield*/, this.file.stat()];
+                    case 2:
+                        fileSize = (_a.sent()).size;
+                        cramContainerHeader1 = sectionParsers.cramContainerHeader1;
+                        i = 0;
+                        _a.label = 3;
+                    case 3:
+                        if (!(i <= containerNumber)) return [3 /*break*/, 11];
+                        // if we are about to go off the end of the file
+                        // and have not found that container, it does not exist
+                        if (position + cramContainerHeader1.maxLength + 8 >= fileSize) {
+                            return [2 /*return*/, undefined];
+                        }
+                        currentContainer = this.getContainerAtPosition(position);
+                        return [4 /*yield*/, currentContainer.getHeader()];
+                    case 4:
+                        currentHeader = _a.sent();
+                        if (!currentHeader) {
+                            throw new errors_1.CramMalformedError("container ".concat(containerNumber, " not found in file"));
+                        }
+                        if (!(i === 0)) return [3 /*break*/, 9];
+                        position = currentHeader._endPosition;
+                        j = 0;
+                        _a.label = 5;
+                    case 5:
+                        if (!(j < currentHeader.numBlocks)) return [3 /*break*/, 8];
+                        return [4 /*yield*/, this.readBlock(position)];
+                    case 6:
+                        block = _a.sent();
+                        position = block._endPosition;
+                        _a.label = 7;
+                    case 7:
+                        j += 1;
+                        return [3 /*break*/, 5];
+                    case 8: return [3 /*break*/, 10];
+                    case 9:
+                        // otherwise, just traverse to the next container using the container's length
+                        position += currentHeader._size + currentHeader.length;
+                        _a.label = 10;
+                    case 10:
+                        i += 1;
+                        return [3 /*break*/, 3];
+                    case 11: return [2 /*return*/, currentContainer];
                 }
-
-                position = currentHeader._endPosition;
-                j = 0;
-
-              case 22:
-                if (!(j < currentHeader.numBlocks)) {
-                  _context5.next = 30;
-                  break;
+            });
+        });
+    };
+    CramFile.prototype.checkCrc32 = function (position, length, recordedCrc32, description) {
+        return __awaiter(this, void 0, void 0, function () {
+            var b, calculatedCrc32;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        b = Buffer.allocUnsafe(length);
+                        return [4 /*yield*/, this.file.read(b, 0, length, position)];
+                    case 1:
+                        _a.sent();
+                        calculatedCrc32 = buffer_crc32_1.default.unsigned(b);
+                        if (calculatedCrc32 !== recordedCrc32) {
+                            throw new errors_1.CramMalformedError("crc mismatch in ".concat(description, ": recorded CRC32 = ").concat(recordedCrc32, ", but calculated CRC32 = ").concat(calculatedCrc32));
+                        }
+                        return [2 /*return*/];
                 }
-
-                _context5.next = 25;
-                return this.readBlock(position);
-
-              case 25:
-                block = _context5.sent;
-                position = block._endPosition;
-
-              case 27:
-                j += 1;
-                _context5.next = 22;
-                break;
-
-              case 30:
-                _context5.next = 33;
-                break;
-
-              case 32:
-                // otherwise, just traverse to the next container using the container's length
-                position += currentHeader._size + currentHeader.length;
-
-              case 33:
-                i += 1;
-                _context5.next = 10;
-                break;
-
-              case 36:
-                return _context5.abrupt("return", currentContainer);
-
-              case 37:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function getContainerById(_x) {
-        return _getContainerById.apply(this, arguments);
-      }
-
-      return getContainerById;
-    }()
-  }, {
-    key: "checkCrc32",
-    value: function () {
-      var _checkCrc = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee6(position, length, recordedCrc32, description) {
-        var b, calculatedCrc32, _context6, _context7;
-
-        return _regenerator.default.wrap(function _callee6$(_context8) {
-          while (1) {
-            switch (_context8.prev = _context8.next) {
-              case 0:
-                b = Buffer.allocUnsafe(length);
-                _context8.next = 3;
-                return this.file.read(b, 0, length, position);
-
-              case 3:
-                calculatedCrc32 = crc32.unsigned(b);
-
-                if (!(calculatedCrc32 !== recordedCrc32)) {
-                  _context8.next = 6;
-                  break;
-                }
-
-                throw new CramMalformedError((0, _concat.default)(_context6 = (0, _concat.default)(_context7 = "crc mismatch in ".concat(description, ": recorded CRC32 = ")).call(_context7, recordedCrc32, ", but calculated CRC32 = ")).call(_context6, calculatedCrc32));
-
-              case 6:
-              case "end":
-                return _context8.stop();
-            }
-          }
-        }, _callee6, this);
-      }));
-
-      function checkCrc32(_x2, _x3, _x4, _x5) {
-        return _checkCrc.apply(this, arguments);
-      }
-
-      return checkCrc32;
-    }()
+            });
+        });
+    };
     /**
      * @returns {Promise[number]} the number of containers in the file
      */
-
-  }, {
-    key: "containerCount",
-    value: function () {
-      var _containerCount = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee7() {
-        var sectionParsers, _ref4, fileSize, cramContainerHeader1, containerCount, position, currentHeader, j, block;
-
-        return _regenerator.default.wrap(function _callee7$(_context9) {
-          while (1) {
-            switch (_context9.prev = _context9.next) {
-              case 0:
-                _context9.next = 2;
-                return this.getSectionParsers();
-
-              case 2:
-                sectionParsers = _context9.sent;
-                _context9.next = 5;
-                return this.file.stat();
-
-              case 5:
-                _ref4 = _context9.sent;
-                fileSize = _ref4.size;
-                cramContainerHeader1 = sectionParsers.cramContainerHeader1;
-                containerCount = 0;
-                position = sectionParsers.cramFileDefinition.maxLength;
-
-              case 10:
-                if (!(position + cramContainerHeader1.maxLength + 8 < fileSize)) {
-                  _context9.next = 33;
-                  break;
+    CramFile.prototype.containerCount = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var sectionParsers, fileSize, cramContainerHeader1, containerCount, position, currentHeader, j, block;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getSectionParsers()];
+                    case 1:
+                        sectionParsers = _a.sent();
+                        return [4 /*yield*/, this.file.stat()];
+                    case 2:
+                        fileSize = (_a.sent()).size;
+                        cramContainerHeader1 = sectionParsers.cramContainerHeader1;
+                        containerCount = 0;
+                        position = sectionParsers.cramFileDefinition.maxLength;
+                        _a.label = 3;
+                    case 3:
+                        if (!(position + cramContainerHeader1.maxLength + 8 < fileSize)) return [3 /*break*/, 11];
+                        return [4 /*yield*/, this.getContainerAtPosition(position).getHeader()];
+                    case 4:
+                        currentHeader = _a.sent();
+                        if (!currentHeader) {
+                            return [3 /*break*/, 11];
+                        }
+                        if (!(containerCount === 0)) return [3 /*break*/, 9];
+                        position = currentHeader._endPosition;
+                        j = 0;
+                        _a.label = 5;
+                    case 5:
+                        if (!(j < currentHeader.numBlocks)) return [3 /*break*/, 8];
+                        return [4 /*yield*/, this.readBlock(position)];
+                    case 6:
+                        block = _a.sent();
+                        position = block._endPosition;
+                        _a.label = 7;
+                    case 7:
+                        j += 1;
+                        return [3 /*break*/, 5];
+                    case 8: return [3 /*break*/, 10];
+                    case 9:
+                        // otherwise, just traverse to the next container using the container's length
+                        position += currentHeader._size + currentHeader.length;
+                        _a.label = 10;
+                    case 10:
+                        containerCount += 1;
+                        return [3 /*break*/, 3];
+                    case 11: return [2 /*return*/, containerCount];
                 }
-
-                _context9.next = 13;
-                return this.getContainerAtPosition(position).getHeader();
-
-              case 13:
-                currentHeader = _context9.sent;
-
-                if (currentHeader) {
-                  _context9.next = 16;
-                  break;
+            });
+        });
+    };
+    CramFile.prototype.getContainerAtPosition = function (position) {
+        return new container_1.default(this, position);
+    };
+    CramFile.prototype.readBlockHeader = function (position) {
+        return __awaiter(this, void 0, void 0, function () {
+            var sectionParsers, cramBlockHeader, fileSize, buffer;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getSectionParsers()];
+                    case 1:
+                        sectionParsers = _a.sent();
+                        cramBlockHeader = sectionParsers.cramBlockHeader;
+                        return [4 /*yield*/, this.file.stat()];
+                    case 2:
+                        fileSize = (_a.sent()).size;
+                        if (position + cramBlockHeader.maxLength >= fileSize) {
+                            return [2 /*return*/, undefined];
+                        }
+                        buffer = Buffer.allocUnsafe(cramBlockHeader.maxLength);
+                        return [4 /*yield*/, this.file.read(buffer, 0, cramBlockHeader.maxLength, position)];
+                    case 3:
+                        _a.sent();
+                        return [2 /*return*/, (0, util_1.parseItem)(buffer, cramBlockHeader.parser, 0, position)];
                 }
-
-                return _context9.abrupt("break", 33);
-
-              case 16:
-                if (!(containerCount === 0)) {
-                  _context9.next = 29;
-                  break;
+            });
+        });
+    };
+    CramFile.prototype._parseSection = function (section, position, size, preReadBuffer) {
+        if (size === void 0) { size = section.maxLength; }
+        return __awaiter(this, void 0, void 0, function () {
+            var buffer, fileSize, data;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        if (!preReadBuffer) return [3 /*break*/, 1];
+                        buffer = preReadBuffer;
+                        return [3 /*break*/, 4];
+                    case 1: return [4 /*yield*/, this.file.stat()];
+                    case 2:
+                        fileSize = (_a.sent()).size;
+                        if (position + size >= fileSize) {
+                            return [2 /*return*/, undefined];
+                        }
+                        buffer = Buffer.allocUnsafe(size);
+                        return [4 /*yield*/, this.file.read(buffer, 0, size, position)];
+                    case 3:
+                        _a.sent();
+                        _a.label = 4;
+                    case 4:
+                        data = (0, util_1.parseItem)(buffer, section.parser, 0, position);
+                        if (data._size !== size) {
+                            throw new errors_1.CramMalformedError("section read error: requested size ".concat(size, " does not equal parsed size ").concat(data._size));
+                        }
+                        return [2 /*return*/, data];
                 }
-
-                position = currentHeader._endPosition;
-                j = 0;
-
-              case 19:
-                if (!(j < currentHeader.numBlocks)) {
-                  _context9.next = 27;
-                  break;
+            });
+        });
+    };
+    CramFile.prototype._uncompress = function (compressionMethod, inputBuffer, outputBuffer) {
+        if (compressionMethod === 'gzip') {
+            var result = zlib_1.default.gunzipSync(inputBuffer);
+            result.copy(outputBuffer);
+        }
+        else if (compressionMethod === 'bzip2') {
+            var bits = bzip2.array(inputBuffer);
+            var size = bzip2.header(bits);
+            var j = 0;
+            do {
+                var chunk = bzip2.decompress(bits, size);
+                if (chunk != -1) {
+                    Buffer.from(chunk).copy(outputBuffer, j);
+                    j += chunk.length;
+                    size -= chunk.length;
                 }
-
-                _context9.next = 22;
-                return this.readBlock(position);
-
-              case 22:
-                block = _context9.sent;
-                position = block._endPosition;
-
-              case 24:
-                j += 1;
-                _context9.next = 19;
-                break;
-
-              case 27:
-                _context9.next = 30;
-                break;
-
-              case 29:
-                // otherwise, just traverse to the next container using the container's length
-                position += currentHeader._size + currentHeader.length;
-
-              case 30:
-                containerCount += 1;
-                _context9.next = 10;
-                break;
-
-              case 33:
-                return _context9.abrupt("return", containerCount);
-
-              case 34:
-              case "end":
-                return _context9.stop();
-            }
-          }
-        }, _callee7, this);
-      }));
-
-      function containerCount() {
-        return _containerCount.apply(this, arguments);
-      }
-
-      return containerCount;
-    }()
-  }, {
-    key: "getContainerAtPosition",
-    value: function getContainerAtPosition(position) {
-      return new CramContainer(this, position);
-    }
-  }, {
-    key: "readBlockHeader",
-    value: function () {
-      var _readBlockHeader = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee8(position) {
-        var sectionParsers, cramBlockHeader, _ref5, fileSize, buffer;
-
-        return _regenerator.default.wrap(function _callee8$(_context10) {
-          while (1) {
-            switch (_context10.prev = _context10.next) {
-              case 0:
-                _context10.next = 2;
-                return this.getSectionParsers();
-
-              case 2:
-                sectionParsers = _context10.sent;
-                cramBlockHeader = sectionParsers.cramBlockHeader;
-                _context10.next = 6;
-                return this.file.stat();
-
-              case 6:
-                _ref5 = _context10.sent;
-                fileSize = _ref5.size;
-
-                if (!(position + cramBlockHeader.maxLength >= fileSize)) {
-                  _context10.next = 10;
-                  break;
+            } while (chunk != -1);
+        }
+        else if (compressionMethod === 'rans') {
+            (0, rans_1.default)(inputBuffer, outputBuffer);
+            //htscodecs r4x8 is slower, but compatible.
+            //htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
+        }
+        else if (compressionMethod === 'rans4x16') {
+            htscodecs_1.default.r4x16_uncompress(inputBuffer, outputBuffer);
+        }
+        else if (compressionMethod === 'arith') {
+            htscodecs_1.default.arith_uncompress(inputBuffer, outputBuffer);
+        }
+        else if (compressionMethod === 'fqzcomp') {
+            htscodecs_1.default.fqzcomp_uncompress(inputBuffer, outputBuffer);
+        }
+        else if (compressionMethod === 'tok3') {
+            htscodecs_1.default.tok3_uncompress(inputBuffer, outputBuffer);
+        }
+        else {
+            throw new errors_1.CramUnimplementedError("".concat(compressionMethod, " decompression not yet implemented"));
+        }
+    };
+    CramFile.prototype.readBlock = function (position) {
+        return __awaiter(this, void 0, void 0, function () {
+            var majorVersion, sectionParsers, block, blockContentPosition, uncompressedData, compressedData, crc;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getDefinition()];
+                    case 1:
+                        majorVersion = (_a.sent()).majorVersion;
+                        return [4 /*yield*/, this.getSectionParsers()];
+                    case 2:
+                        sectionParsers = _a.sent();
+                        return [4 /*yield*/, this.readBlockHeader(position)];
+                    case 3:
+                        block = _a.sent();
+                        blockContentPosition = block._endPosition;
+                        block.contentPosition = block._endPosition;
+                        uncompressedData = Buffer.allocUnsafe(block.uncompressedSize);
+                        if (!(block.compressionMethod !== 'raw')) return [3 /*break*/, 5];
+                        compressedData = Buffer.allocUnsafe(block.compressedSize);
+                        return [4 /*yield*/, this.read(compressedData, 0, block.compressedSize, blockContentPosition)];
+                    case 4:
+                        _a.sent();
+                        this._uncompress(block.compressionMethod, compressedData, uncompressedData);
+                        return [3 /*break*/, 7];
+                    case 5: return [4 /*yield*/, this.read(uncompressedData, 0, block.uncompressedSize, blockContentPosition)];
+                    case 6:
+                        _a.sent();
+                        _a.label = 7;
+                    case 7:
+                        block.content = uncompressedData;
+                        if (!(majorVersion >= 3)) return [3 /*break*/, 11];
+                        return [4 /*yield*/, this._parseSection(sectionParsers.cramBlockCrc32, blockContentPosition + block.compressedSize)];
+                    case 8:
+                        crc = _a.sent();
+                        block.crc32 = crc.crc32;
+                        if (!this.validateChecksums) return [3 /*break*/, 10];
+                        return [4 /*yield*/, this.checkCrc32(position, block._size + block.compressedSize, block.crc32, 'block data')];
+                    case 9:
+                        _a.sent();
+                        _a.label = 10;
+                    case 10:
+                        // make the endposition and size reflect the whole block
+                        block._endPosition = crc._endPosition;
+                        block._size =
+                            block.compressedSize + sectionParsers.cramBlockCrc32.maxLength;
+                        return [3 /*break*/, 12];
+                    case 11:
+                        block._endPosition = blockContentPosition + block.compressedSize;
+                        block._size = block.compressedSize;
+                        _a.label = 12;
+                    case 12: return [2 /*return*/, block];
                 }
-
-                return _context10.abrupt("return", undefined);
-
-              case 10:
-                buffer = Buffer.allocUnsafe(cramBlockHeader.maxLength);
-                _context10.next = 13;
-                return this.file.read(buffer, 0, cramBlockHeader.maxLength, position);
-
-              case 13:
-                return _context10.abrupt("return", parseItem(buffer, cramBlockHeader.parser, 0, position));
-
-              case 14:
-              case "end":
-                return _context10.stop();
-            }
-          }
-        }, _callee8, this);
-      }));
-
-      function readBlockHeader(_x6) {
-        return _readBlockHeader.apply(this, arguments);
-      }
-
-      return readBlockHeader;
-    }()
-  }, {
-    key: "_parseSection",
-    value: function () {
-      var _parseSection2 = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee9(section, position) {
-        var _context11;
-
-        var size,
-            preReadBuffer,
-            buffer,
-            _ref6,
-            fileSize,
-            data,
-            _args9 = arguments;
-
-        return _regenerator.default.wrap(function _callee9$(_context12) {
-          while (1) {
-            switch (_context12.prev = _context12.next) {
-              case 0:
-                size = _args9.length > 2 && _args9[2] !== undefined ? _args9[2] : section.maxLength;
-                preReadBuffer = _args9.length > 3 ? _args9[3] : undefined;
-
-                if (!preReadBuffer) {
-                  _context12.next = 6;
-                  break;
-                }
-
-                buffer = preReadBuffer;
-                _context12.next = 15;
-                break;
-
-              case 6:
-                _context12.next = 8;
-                return this.file.stat();
-
-              case 8:
-                _ref6 = _context12.sent;
-                fileSize = _ref6.size;
-
-                if (!(position + size >= fileSize)) {
-                  _context12.next = 12;
-                  break;
-                }
-
-                return _context12.abrupt("return", undefined);
-
-              case 12:
-                buffer = Buffer.allocUnsafe(size);
-                _context12.next = 15;
-                return this.file.read(buffer, 0, size, position);
-
-              case 15:
-                data = parseItem(buffer, section.parser, 0, position);
-
-                if (!(data._size !== size)) {
-                  _context12.next = 18;
-                  break;
-                }
-
-                throw new CramMalformedError((0, _concat.default)(_context11 = "section read error: requested size ".concat(size, " does not equal parsed size ")).call(_context11, data._size));
-
-              case 18:
-                return _context12.abrupt("return", data);
-
-              case 19:
-              case "end":
-                return _context12.stop();
-            }
-          }
-        }, _callee9, this);
-      }));
-
-      function _parseSection(_x7, _x8) {
-        return _parseSection2.apply(this, arguments);
-      }
-
-      return _parseSection;
-    }()
-  }, {
-    key: "_uncompress",
-    value: function _uncompress(compressionMethod, inputBuffer, outputBuffer) {
-      if (compressionMethod === 'gzip') {
-        var result = zlib.gunzipSync(inputBuffer);
-        result.copy(outputBuffer);
-      } else if (compressionMethod === 'rans') {
-        rans.uncompress(inputBuffer, outputBuffer);
-      } else {
-        throw new CramUnimplementedError("".concat(compressionMethod, " decompression not yet implemented"));
-      }
-    }
-  }, {
-    key: "readBlock",
-    value: function () {
-      var _readBlock = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee10(position) {
-        var _ref7, majorVersion, sectionParsers, block, blockContentPosition, uncompressedData, compressedData, crc;
-
-        return _regenerator.default.wrap(function _callee10$(_context13) {
-          while (1) {
-            switch (_context13.prev = _context13.next) {
-              case 0:
-                _context13.next = 2;
-                return this.getDefinition();
-
-              case 2:
-                _ref7 = _context13.sent;
-                majorVersion = _ref7.majorVersion;
-                _context13.next = 6;
-                return this.getSectionParsers();
-
-              case 6:
-                sectionParsers = _context13.sent;
-                _context13.next = 9;
-                return this.readBlockHeader(position);
-
-              case 9:
-                block = _context13.sent;
-                blockContentPosition = block._endPosition;
-                block.contentPosition = block._endPosition;
-                uncompressedData = Buffer.allocUnsafe(block.uncompressedSize);
-
-                if (!(block.compressionMethod !== 'raw')) {
-                  _context13.next = 20;
-                  break;
-                }
-
-                compressedData = Buffer.allocUnsafe(block.compressedSize);
-                _context13.next = 17;
-                return this.read(compressedData, 0, block.compressedSize, blockContentPosition);
-
-              case 17:
-                this._uncompress(block.compressionMethod, compressedData, uncompressedData);
-
-                _context13.next = 22;
-                break;
-
-              case 20:
-                _context13.next = 22;
-                return this.read(uncompressedData, 0, block.uncompressedSize, blockContentPosition);
-
-              case 22:
-                block.content = uncompressedData;
-
-                if (!(majorVersion >= 3)) {
-                  _context13.next = 35;
-                  break;
-                }
-
-                _context13.next = 26;
-                return this._parseSection(sectionParsers.cramBlockCrc32, blockContentPosition + block.compressedSize);
-
-              case 26:
-                crc = _context13.sent;
-                block.crc32 = crc.crc32; // check the block data crc32
-
-                if (!this.validateChecksums) {
-                  _context13.next = 31;
-                  break;
-                }
-
-                _context13.next = 31;
-                return this.checkCrc32(position, block._size + block.compressedSize, block.crc32, 'block data');
-
-              case 31:
-                // make the endposition and size reflect the whole block
-                block._endPosition = crc._endPosition;
-                block._size = block.compressedSize + sectionParsers.cramBlockCrc32.maxLength;
-                _context13.next = 37;
-                break;
-
-              case 35:
-                block._endPosition = blockContentPosition + block.compressedSize;
-                block._size = block.compressedSize;
-
-              case 37:
-                return _context13.abrupt("return", block);
-
-              case 38:
-              case "end":
-                return _context13.stop();
-            }
-          }
-        }, _callee10, this);
-      }));
-
-      function readBlock(_x9) {
-        return _readBlock.apply(this, arguments);
-      }
-
-      return readBlock;
-    }()
-  }]);
-  return CramFile;
-}();
-
-(0, _forEach.default)(_context14 = 'getDefinition getSectionParsers getSamHeader'.split(' ')).call(_context14, function (method) {
-  return tinyMemoize(CramFile, method);
-});
-module.exports = CramFile;
+            });
+        });
+    };
+    return CramFile;
+}());
+exports.default = CramFile;
+'getDefinition getSectionParsers getSamHeader'
+    .split(' ')
+    .forEach(function (method) { return (0, util_1.tinyMemoize)(CramFile, method); });
+//# sourceMappingURL=file.js.map

dist/cramFile/index.js

 "use strict";
-
-var CramFile = require('./file');
-
-module.exports = CramFile;
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var file_1 = __importDefault(require("./file"));
+exports.default = file_1.default;
+//# sourceMappingURL=index.js.map

dist/cramFile/record.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _keys = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/keys"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _flags = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/flags"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/toConsumableArray"));
-
-var Constants = require('./constants');
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var constants_1 = __importDefault(require("./constants"));
 function decodeReadSequence(cramRecord, refRegion) {
-  // if it has no length, it has no sequence
-  if (!cramRecord.lengthOnRef && !cramRecord.readLength) return undefined;
-  if (cramRecord.isUnknownBases()) return undefined; // remember: all coordinates are 1-based closed
-
-  var regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
-  if (!cramRecord.readFeatures) return refRegion.seq.substr(regionSeqOffset, cramRecord.lengthOnRef).toUpperCase();
-  var bases = '';
-  var regionPos = regionSeqOffset;
-  var currentReadFeature = 0;
-
-  while (bases.length < cramRecord.readLength) {
-    if (currentReadFeature < cramRecord.readFeatures.length) {
-      var feature = cramRecord.readFeatures[currentReadFeature];
-
-      if (feature.code === 'Q' || feature.code === 'q') {
-        currentReadFeature += 1;
-      } else if (feature.pos === bases.length + 1) {
-        // process the read feature
-        currentReadFeature += 1;
-
-        if (feature.code === 'b') {
-          // specify a base pair for some reason
-          var ret = feature.data.split(',');
-          var added = String.fromCharCode.apply(String, (0, _toConsumableArray2.default)(ret));
-          bases += added;
-          regionPos += added.length;
-        } else if (feature.code === 'B') {
-          // base pair and associated quality
-          // TODO: do we need to set the quality in the qual scores?
-          bases += feature.data[0];
-          regionPos += 1;
-        } else if (feature.code === 'X') {
-          // base substitution
-          bases += feature.sub;
-          regionPos += 1;
-        } else if (feature.code === 'I') {
-          // insertion
-          bases += feature.data;
-        } else if (feature.code === 'D') {
-          // deletion
-          regionPos += feature.data;
-        } else if (feature.code === 'i') {
-          // insert single base
-          bases += feature.data;
-        } else if (feature.code === 'N') {
-          // reference skip. delete some bases
-          // do nothing
-          // seqBases.splice(feature.pos - 1, feature.data)
-          regionPos += feature.data;
-        } else if (feature.code === 'S') {
-          // soft clipped bases that should be present in the read seq
-          // seqBases.splice(feature.pos - 1, 0, ...feature.data.split(''))
-          bases += feature.data;
-        } else if (feature.code === 'P') {// padding, do nothing
-        } else if (feature.code === 'H') {// hard clip, do nothing
+    // if it has no length, it has no sequence
+    if (!cramRecord.lengthOnRef && !cramRecord.readLength) {
+        return undefined;
+    }
+    if (cramRecord.isUnknownBases()) {
+        return undefined;
+    }
+    // remember: all coordinates are 1-based closed
+    var regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
+    if (!cramRecord.readFeatures) {
+        return refRegion.seq
+            .substr(regionSeqOffset, cramRecord.lengthOnRef)
+            .toUpperCase();
+    }
+    var bases = '';
+    var regionPos = regionSeqOffset;
+    var currentReadFeature = 0;
+    while (bases.length < cramRecord.readLength) {
+        if (currentReadFeature < cramRecord.readFeatures.length) {
+            var feature = cramRecord.readFeatures[currentReadFeature];
+            if (feature.code === 'Q' || feature.code === 'q') {
+                currentReadFeature += 1;
+            }
+            else if (feature.pos === bases.length + 1) {
+                // process the read feature
+                currentReadFeature += 1;
+                if (feature.code === 'b') {
+                    // specify a base pair for some reason
+                    var ret = feature.data.split(',');
+                    var added = String.fromCharCode.apply(String, ret);
+                    bases += added;
+                    regionPos += added.length;
+                }
+                else if (feature.code === 'B') {
+                    // base pair and associated quality
+                    // TODO: do we need to set the quality in the qual scores?
+                    bases += feature.data[0];
+                    regionPos += 1;
+                }
+                else if (feature.code === 'X') {
+                    // base substitution
+                    bases += feature.sub;
+                    regionPos += 1;
+                }
+                else if (feature.code === 'I') {
+                    // insertion
+                    bases += feature.data;
+                }
+                else if (feature.code === 'D') {
+                    // deletion
+                    regionPos += feature.data;
+                }
+                else if (feature.code === 'i') {
+                    // insert single base
+                    bases += feature.data;
+                }
+                else if (feature.code === 'N') {
+                    // reference skip. delete some bases
+                    // do nothing
+                    // seqBases.splice(feature.pos - 1, feature.data)
+                    regionPos += feature.data;
+                }
+                else if (feature.code === 'S') {
+                    // soft clipped bases that should be present in the read seq
+                    // seqBases.splice(feature.pos - 1, 0, ...feature.data.split(''))
+                    bases += feature.data;
+                }
+                else if (feature.code === 'P') {
+                    // padding, do nothing
+                }
+                else if (feature.code === 'H') {
+                    // hard clip, do nothing
+                }
+            }
+            else if (currentReadFeature < cramRecord.readFeatures.length) {
+                // put down a chunk of sequence up to the next read feature
+                var chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
+                bases += chunk;
+                regionPos += chunk.length;
+            }
         }
-      } else if (currentReadFeature < cramRecord.readFeatures.length) {
-        // put down a chunk of sequence up to the next read feature
-        var chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
-        bases += chunk;
-        regionPos += chunk.length;
-      }
-    } else {
-      // put down a chunk of reference up to the full read length
-      var _chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
-
-      bases += _chunk;
-      regionPos += _chunk.length;
+        else {
+            // put down a chunk of reference up to the full read length
+            var chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
+            bases += chunk;
+            regionPos += chunk.length;
+        }
     }
-  }
-
-  return bases.toUpperCase();
+    return bases.toUpperCase();
 }
-
 var baseNumbers = {
-  a: 0,
-  A: 0,
-  c: 1,
-  C: 1,
-  g: 2,
-  G: 2,
-  t: 3,
-  T: 3,
-  n: 4,
-  N: 4
+    a: 0,
+    A: 0,
+    c: 1,
+    C: 1,
+    g: 2,
+    G: 2,
+    t: 3,
+    T: 3,
+    n: 4,
+    N: 4,
 };
-
 function decodeBaseSubstitution(cramRecord, refRegion, compressionScheme, readFeature) {
-  if (!refRegion) return; // decode base substitution code using the substitution matrix
-
-  var refCoord = readFeature.refPos - refRegion.start;
-  var refBase = refRegion.seq.charAt(refCoord);
-  if (refBase) readFeature.ref = refBase;
-  var baseNumber = baseNumbers[refBase];
-  if (baseNumber === undefined) baseNumber = 4;
-  var substitutionScheme = compressionScheme.substitutionMatrix[baseNumber];
-  var base = substitutionScheme[readFeature.data];
-  if (base) readFeature.sub = base;
+    if (!refRegion) {
+        return;
+    }
+    // decode base substitution code using the substitution matrix
+    var refCoord = readFeature.refPos - refRegion.start;
+    var refBase = refRegion.seq.charAt(refCoord);
+    if (refBase) {
+        readFeature.ref = refBase;
+    }
+    var baseNumber = baseNumbers[refBase];
+    if (baseNumber === undefined) {
+        baseNumber = 4;
+    }
+    var substitutionScheme = compressionScheme.substitutionMatrix[baseNumber];
+    var base = substitutionScheme[readFeature.data];
+    if (base) {
+        readFeature.sub = base;
+    }
 }
@@ -122,128 +133,74 @@ /**
  */
-
-
-var CramRecord =
-/*#__PURE__*/
-function () {
-  function CramRecord() {
-    (0, _classCallCheck2.default)(this, CramRecord);
-    this.tags = {};
-  }
-  /**
-   * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
-   */
-
-
-  (0, _createClass2.default)(CramRecord, [{
-    key: "isPaired",
-    value: function isPaired() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FPAIRED);
+var CramRecord = /** @class */ (function () {
+    function CramRecord() {
+        this.tags = {};
     }
+    /**
+     * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
+     */
+    CramRecord.prototype.isPaired = function () {
+        return !!(this.flags & constants_1.default.BAM_FPAIRED);
+    };
     /** @returns {boolean} true if the read is paired, and both segments are mapped */
-
-  }, {
-    key: "isProperlyPaired",
-    value: function isProperlyPaired() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FPROPER_PAIR);
-    }
+    CramRecord.prototype.isProperlyPaired = function () {
+        return !!(this.flags & constants_1.default.BAM_FPROPER_PAIR);
+    };
     /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-
-  }, {
-    key: "isSegmentUnmapped",
-    value: function isSegmentUnmapped() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FUNMAP);
-    }
+    CramRecord.prototype.isSegmentUnmapped = function () {
+        return !!(this.flags & constants_1.default.BAM_FUNMAP);
+    };
     /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-
-  }, {
-    key: "isMateUnmapped",
-    value: function isMateUnmapped() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FMUNMAP);
-    }
+    CramRecord.prototype.isMateUnmapped = function () {
+        return !!(this.flags & constants_1.default.BAM_FMUNMAP);
+    };
     /** @returns {boolean} true if the read is mapped to the reverse strand */
-
-  }, {
-    key: "isReverseComplemented",
-    value: function isReverseComplemented() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FREVERSE);
-    }
+    CramRecord.prototype.isReverseComplemented = function () {
+        return !!(this.flags & constants_1.default.BAM_FREVERSE);
+    };
     /** @returns {boolean} true if the mate is mapped to the reverse strand */
-
-  }, {
-    key: "isMateReverseComplemented",
-    value: function isMateReverseComplemented() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FMREVERSE);
-    }
+    CramRecord.prototype.isMateReverseComplemented = function () {
+        return !!(this.flags & constants_1.default.BAM_FMREVERSE);
+    };
     /** @returns {boolean} true if this is read number 1 in a pair */
-
-  }, {
-    key: "isRead1",
-    value: function isRead1() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FREAD1);
-    }
+    CramRecord.prototype.isRead1 = function () {
+        return !!(this.flags & constants_1.default.BAM_FREAD1);
+    };
     /** @returns {boolean} true if this is read number 2 in a pair */
-
-  }, {
-    key: "isRead2",
-    value: function isRead2() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FREAD2);
-    }
+    CramRecord.prototype.isRead2 = function () {
+        return !!(this.flags & constants_1.default.BAM_FREAD2);
+    };
     /** @returns {boolean} true if this is a secondary alignment */
-
-  }, {
-    key: "isSecondary",
-    value: function isSecondary() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FSECONDARY);
-    }
+    CramRecord.prototype.isSecondary = function () {
+        return !!(this.flags & constants_1.default.BAM_FSECONDARY);
+    };
     /** @returns {boolean} true if this read has failed QC checks */
-
-  }, {
-    key: "isFailedQc",
-    value: function isFailedQc() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FQCFAIL);
-    }
+    CramRecord.prototype.isFailedQc = function () {
+        return !!(this.flags & constants_1.default.BAM_FQCFAIL);
+    };
     /** @returns {boolean} true if the read is an optical or PCR duplicate */
-
-  }, {
-    key: "isDuplicate",
-    value: function isDuplicate() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FDUP);
-    }
+    CramRecord.prototype.isDuplicate = function () {
+        return !!(this.flags & constants_1.default.BAM_FDUP);
+    };
     /** @returns {boolean} true if this is a supplementary alignment */
-
-  }, {
-    key: "isSupplementary",
-    value: function isSupplementary() {
-      return !!((0, _flags.default)(this) & Constants.BAM_FSUPPLEMENTARY);
-    }
+    CramRecord.prototype.isSupplementary = function () {
+        return !!(this.flags & constants_1.default.BAM_FSUPPLEMENTARY);
+    };
     /**
      * @returns {boolean} true if the read is detached
      */
-
-  }, {
-    key: "isDetached",
-    value: function isDetached() {
-      return !!(this.cramFlags & Constants.CRAM_FLAG_DETACHED);
-    }
+    CramRecord.prototype.isDetached = function () {
+        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_DETACHED);
+    };
     /** @returns {boolean} true if the read has a mate in this same CRAM segment */
-
-  }, {
-    key: "hasMateDownStream",
-    value: function hasMateDownStream() {
-      return !!(this.cramFlags & Constants.CRAM_FLAG_MATE_DOWNSTREAM);
-    }
+    CramRecord.prototype.hasMateDownStream = function () {
+        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_MATE_DOWNSTREAM);
+    };
     /** @returns {boolean} true if the read contains qual scores */
-
-  }, {
-    key: "isPreservingQualityScores",
-    value: function isPreservingQualityScores() {
-      return !!(this.cramFlags & Constants.CRAM_FLAG_PRESERVE_QUAL_SCORES);
-    }
+    CramRecord.prototype.isPreservingQualityScores = function () {
+        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_PRESERVE_QUAL_SCORES);
+    };
     /** @returns {boolean} true if the read has no sequence bases */
-
-  }, {
-    key: "isUnknownBases",
-    value: function isUnknownBases() {
-      return !!(this.cramFlags & Constants.CRAM_FLAG_NO_SEQ);
-    }
+    CramRecord.prototype.isUnknownBases = function () {
+        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_NO_SEQ);
+    };
     /**
@@ -253,12 +210,8 @@ * Get the original sequence of this read.
      */
-
-  }, {
-    key: "getReadBases",
-    value: function getReadBases() {
-      if (!this.readBases && this._refRegion) {
-        this.readBases = decodeReadSequence(this, this._refRegion);
-      }
-
-      return this.readBases;
-    }
+    CramRecord.prototype.getReadBases = function () {
+        if (!this.readBases && this._refRegion) {
+            this.readBases = decodeReadSequence(this, this._refRegion);
+        }
+        return this.readBases;
+    };
     /**
@@ -268,44 +221,41 @@ * Get the pair orientation of a paired read. Adapted from igv.js
      */
-
-  }, {
-    key: "getPairOrientation",
-    value: function getPairOrientation() {
-      if (!this.isSegmentUnmapped() && this.isPaired() && !this.isMateUnmapped() && this.mate && this.sequenceId === this.mate.sequenceId) {
-        var s1 = this.isReverseComplemented() ? 'R' : 'F';
-        var s2 = this.isMateReverseComplemented() ? 'R' : 'F';
-        var o1 = ' ';
-        var o2 = ' ';
-
-        if (this.isRead1()) {
-          o1 = '1';
-          o2 = '2';
-        } else if (this.isRead2()) {
-          o1 = '2';
-          o2 = '1';
+    CramRecord.prototype.getPairOrientation = function () {
+        if (!this.isSegmentUnmapped() &&
+            this.isPaired() &&
+            !this.isMateUnmapped() &&
+            this.mate &&
+            this.sequenceId === this.mate.sequenceId) {
+            var s1 = this.isReverseComplemented() ? 'R' : 'F';
+            var s2 = this.isMateReverseComplemented() ? 'R' : 'F';
+            var o1 = ' ';
+            var o2 = ' ';
+            if (this.isRead1()) {
+                o1 = '1';
+                o2 = '2';
+            }
+            else if (this.isRead2()) {
+                o1 = '2';
+                o2 = '1';
+            }
+            var tmp = [];
+            var isize = this.templateLength || this.templateSize;
+            if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
+                isize = -isize;
+            }
+            if (isize > 0) {
+                tmp[0] = s1;
+                tmp[1] = o1;
+                tmp[2] = s2;
+                tmp[3] = o2;
+            }
+            else {
+                tmp[2] = s1;
+                tmp[3] = o1;
+                tmp[0] = s2;
+                tmp[1] = o2;
+            }
+            return tmp.join('');
         }
-
-        var tmp = [];
-        var isize = this.templateLength || this.templateSize;
-
-        if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
-          isize = -isize;
-        }
-
-        if (isize > 0) {
-          tmp[0] = s1;
-          tmp[1] = o1;
-          tmp[2] = s2;
-          tmp[3] = o2;
-        } else {
-          tmp[2] = s1;
-          tmp[3] = o1;
-          tmp[0] = s2;
-          tmp[1] = o2;
-        }
-
-        return tmp.join('');
-      }
-
-      return null;
-    }
+        return null;
+    };
     /**
@@ -324,42 +274,37 @@ * Annotates this feature with the given reference sequence basepair
      */
-
-  }, {
-    key: "addReferenceSequence",
-    value: function addReferenceSequence(refRegion, compressionScheme) {
-      var _this = this;
-
-      if (this.readFeatures) {
-        var _context;
-
-        // use the reference bases to decode the bases
-        // substituted in each base substitution
-        (0, _forEach.default)(_context = this.readFeatures).call(_context, function (readFeature) {
-          if (readFeature.code === 'X') decodeBaseSubstitution(_this, refRegion, compressionScheme, readFeature);
+    CramRecord.prototype.addReferenceSequence = function (refRegion, compressionScheme) {
+        var _this = this;
+        if (this.readFeatures) {
+            // use the reference bases to decode the bases
+            // substituted in each base substitution
+            this.readFeatures.forEach(function (readFeature) {
+                if (readFeature.code === 'X') {
+                    decodeBaseSubstitution(_this, refRegion, compressionScheme, readFeature);
+                }
+            });
+        }
+        // if this region completely covers this read,
+        // keep a reference to it
+        if (!this.readBases &&
+            refRegion.start <= this.alignmentStart &&
+            refRegion.end >=
+                this.alignmentStart + (this.lengthOnRef || this.readLength) - 1) {
+            this._refRegion = refRegion;
+        }
+    };
+    CramRecord.prototype.toJSON = function () {
+        var _this = this;
+        var data = {};
+        Object.keys(this).forEach(function (k) {
+            if (k.charAt(0) === '_') {
+                return;
+            }
+            data[k] = _this[k];
         });
-      } // if this region completely covers this read,
-      // keep a reference to it
-
-
-      if (!this.readBases && refRegion.start <= this.alignmentStart && refRegion.end >= this.alignmentStart + (this.lengthOnRef || this.readLength) - 1) {
-        this._refRegion = refRegion;
-      }
-    }
-  }, {
-    key: "toJSON",
-    value: function toJSON() {
-      var _context2,
-          _this2 = this;
-
-      var data = {};
-      (0, _forEach.default)(_context2 = (0, _keys.default)(this)).call(_context2, function (k) {
-        if (k.charAt(0) === '_') return;
-        data[k] = _this2[k];
-      });
-      data.readBases = this.getReadBases();
-      return data;
-    }
-  }]);
-  return CramRecord;
-}();
-
-module.exports = CramRecord;
+        data.readBases = this.getReadBases();
+        return data;
+    };
+    return CramRecord;
+}());
+exports.default = CramRecord;
+//# sourceMappingURL=record.js.map

dist/cramFile/sectionParsers.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _keys = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/keys"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _assign = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/assign"));
-
-var _require = require('@gmod/binary-parser'),
-    Parser = _require.Parser;
-
-var singleItf8 = new Parser().itf8();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getSectionParsers = exports.cramFileDefinition = void 0;
+var binary_parser_1 = require("@gmod/binary-parser");
+var singleItf8 = new binary_parser_1.Parser().itf8();
 var cramFileDefinition = {
-  parser: new Parser().string('magic', {
-    length: 4
-  }).uint8('majorVersion').uint8('minorVersion').string('fileId', {
-    length: 20,
-    stripNull: true
-  }),
-  maxLength: 26
+    parser: new binary_parser_1.Parser()
+        .string('magic', { length: 4 })
+        .uint8('majorVersion')
+        .uint8('minorVersion')
+        .string('fileId', { length: 20, stripNull: true }),
+    maxLength: 26,
 };
+exports.cramFileDefinition = cramFileDefinition;
 var cramBlockHeader = {
-  parser: new Parser().uint8('compressionMethod', {
-    formatter:
-    /* istanbul ignore next */
-    function formatter(b) {
-      var method = ['raw', 'gzip', 'bzip2', 'lzma', 'rans'][b];
-      if (!method) throw new Error("compression method number ".concat(b, " not implemented"));
-      return method;
-    }
-  }).uint8('contentType', {
-    formatter:
-    /* istanbul ignore next */
-    function formatter(b) {
-      var type = ['FILE_HEADER', 'COMPRESSION_HEADER', 'MAPPED_SLICE_HEADER', 'UNMAPPED_SLICE_HEADER', // < only used in cram v1
-      'EXTERNAL_DATA', 'CORE_DATA'][b];
-      if (!type) throw new Error("invalid block content type id ".concat(b));
-      return type;
-    }
-  }).itf8('contentId').itf8('compressedSize').itf8('uncompressedSize'),
-  maxLength: 17
+    parser: new binary_parser_1.Parser()
+        .uint8('compressionMethod', {
+        formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ b) {
+            var method = [
+                'raw',
+                'gzip',
+                'bzip2',
+                'lzma',
+                'rans',
+                'rans4x16',
+                'arith',
+                'fqzcomp',
+                'tok3',
+            ][b];
+            if (!method) {
+                throw new Error("compression method number ".concat(b, " not implemented"));
+            }
+            return method;
+        },
+    })
+        .uint8('contentType', {
+        formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ b) {
+            var type = [
+                'FILE_HEADER',
+                'COMPRESSION_HEADER',
+                'MAPPED_SLICE_HEADER',
+                'UNMAPPED_SLICE_HEADER',
+                'EXTERNAL_DATA',
+                'CORE_DATA',
+            ][b];
+            if (!type) {
+                throw new Error("invalid block content type id ".concat(b));
+            }
+            return type;
+        },
+    })
+        .itf8('contentId')
+        .itf8('compressedSize')
+        .itf8('uncompressedSize'),
+    maxLength: 17,
 };
 var cramBlockCrc32 = {
-  parser: new Parser().uint32('crc32'),
-  maxLength: 4
-}; // const ENCODING_NAMES = [
+    parser: new binary_parser_1.Parser().uint32('crc32'),
+    maxLength: 4,
+};
+// const ENCODING_NAMES = [
 //   'NULL', // 0
@@ -60,332 +73,281 @@ //   'EXTERNAL', // 1
 // ]
-
-var cramTagDictionary = new Parser().itf8('size').buffer('ents', {
-  length: 'size',
-  formatter:
-  /* istanbul ignore next */
-  function formatter(buffer) {
-    function makeTagSet(stringStart, stringEnd) {
-      var str = buffer.toString('utf8', stringStart, stringEnd);
-      var tags = [];
-
-      for (var _i = 0; _i < str.length; _i += 3) {
-        tags.push(str.substr(_i, 3));
-      }
-
-      return tags;
-    }
-    /* eslint-disable */
-
-
-    var tagSets = [];
-    var stringStart = 0;
-    var i;
-    /* eslint-enable */
-
-    for (i = 0; i < buffer.length; i += 1) {
-      if (!buffer[i]) {
-        tagSets.push(makeTagSet(stringStart, i));
-        stringStart = i + 1;
-      }
-    }
-
-    if (i > stringStart) tagSets.push(makeTagSet(stringStart, i));
-    return tagSets;
-  }
-}); // const cramPreservationMapKeys = 'XX RN AP RR SM TD'.split(' ')
-
-var parseByteAsBool = new Parser().uint8(null, {
-  formatter:
-  /* istanbul ignore next */
-  function formatter(val) {
-    return !!val;
-  }
-});
-var cramPreservationMap = new Parser().itf8('mapSize').itf8('mapCount').array('ents', {
-  length: 'mapCount',
-  type: new Parser().string('key', {
-    length: 2,
-    stripNull: false // formatter: val => cramPreservationMapKeys[val] || 0,
-
-  }).choice('value', {
-    tag: 'key',
-    choices: {
-      MI: parseByteAsBool,
-      UI: parseByteAsBool,
-      PI: parseByteAsBool,
-      RN: parseByteAsBool,
-      AP: parseByteAsBool,
-      RR: parseByteAsBool,
-      SM: new Parser().array(null, {
-        type: 'uint8',
-        length: 5
-      }),
-      TD: new Parser().nest(null, {
-        type: cramTagDictionary,
-        formatter:
-        /* istanbul ignore next */
-        function formatter(data) {
-          return data.ents;
+var cramTagDictionary = new binary_parser_1.Parser().itf8('size').buffer('ents', {
+    length: 'size',
+    formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ buffer) {
+        function makeTagSet(stringStart, stringEnd) {
+            var str = buffer.toString('utf8', stringStart, stringEnd);
+            var tags = [];
+            for (var i_1 = 0; i_1 < str.length; i_1 += 3) {
+                tags.push(str.substr(i_1, 3));
+            }
+            return tags;
         }
-      })
-    }
-  })
+        /* eslint-disable */
+        var tagSets = [];
+        var stringStart = 0;
+        var i;
+        /* eslint-enable */
+        for (i = 0; i < buffer.length; i += 1) {
+            if (!buffer[i]) {
+                tagSets.push(makeTagSet(stringStart, i));
+                stringStart = i + 1;
+            }
+        }
+        if (i > stringStart) {
+            tagSets.push(makeTagSet(stringStart, i));
+        }
+        return tagSets;
+    },
 });
+// const cramPreservationMapKeys = 'XX RN AP RR SM TD'.split(' ')
+var parseByteAsBool = new binary_parser_1.Parser().uint8(null, {
+    formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ val) { return !!val; },
+});
+var cramPreservationMap = new binary_parser_1.Parser()
+    .itf8('mapSize')
+    .itf8('mapCount')
+    .array('ents', {
+    length: 'mapCount',
+    type: new binary_parser_1.Parser()
+        .string('key', {
+        length: 2,
+        stripNull: false,
+        // formatter: val => cramPreservationMapKeys[val] || 0,
+    })
+        .choice('value', {
+        tag: 'key',
+        choices: {
+            MI: parseByteAsBool,
+            UI: parseByteAsBool,
+            PI: parseByteAsBool,
+            RN: parseByteAsBool,
+            AP: parseByteAsBool,
+            RR: parseByteAsBool,
+            SM: new binary_parser_1.Parser().array(null, { type: 'uint8', length: 5 }),
+            TD: new binary_parser_1.Parser().nest(null, {
+                type: cramTagDictionary,
+                formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ data) { return data.ents; },
+            }),
+        },
+    }),
+});
 /* istanbul ignore next */
-
 function formatMap(data) {
-  var map = {};
-
-  for (var i = 0; i < data.ents.length; i += 1) {
-    var _data$ents$i = data.ents[i],
-        key = _data$ents$i.key,
-        value = _data$ents$i.value;
-    if (map[key]) console.warn("duplicate key ".concat(key, " in map"));
-    map[key] = value;
-  }
-
-  return map;
+    var map = {};
+    for (var i = 0; i < data.ents.length; i += 1) {
+        var _a = data.ents[i], key = _a.key, value = _a.value;
+        if (map[key]) {
+            console.warn("duplicate key ".concat(key, " in map"));
+        }
+        map[key] = value;
+    }
+    return map;
 }
-
 var unversionedParsers = {
-  cramFileDefinition: cramFileDefinition,
-  cramBlockHeader: cramBlockHeader,
-  cramBlockCrc32: cramBlockCrc32
-}; // each of these is a function of the major and minor version
-
+    cramFileDefinition: cramFileDefinition,
+    cramBlockHeader: cramBlockHeader,
+    cramBlockCrc32: cramBlockCrc32,
+};
+// each of these is a function of the major and minor version
 var versionedParsers = {
-  // assemble a section parser for the unmapped slice header, with slight
-  // variations depending on the major version of the cram file
-  cramUnmappedSliceHeader: function cramUnmappedSliceHeader(majorVersion) {
-    var maxLength = 0;
-    var parser = new Parser().itf8('numRecords');
-    maxLength += 5; // recordCounter is itf8 in a CRAM v2 file, absent in CRAM v1
-
-    if (majorVersion >= 3) {
-      parser = parser.ltf8('recordCounter');
-      maxLength += 9;
-    } else if (majorVersion === 2) {
-      parser = parser.itf8('recordCounter');
-      maxLength += 5;
-    }
-
-    parser = parser.itf8('numBlocks').itf8('numContentIds').array('contentIds', {
-      type: singleItf8,
-      length: 'numContentIds'
-    });
-    maxLength += 5 * 2; // + numContentIds*5
-    // the md5 sum is missing in cram v1
-
-    if (majorVersion >= 2) {
-      parser = parser.array('md5', {
-        type: 'uint8',
-        length: 16
-      });
-      maxLength += 16;
-    }
-
-    var maxLengthFunc = function maxLengthFunc(numContentIds) {
-      return maxLength + numContentIds * 5;
-    };
-
-    return {
-      parser: parser,
-      maxLength: maxLengthFunc
-    }; // : p, maxLength: numContentIds => 5 + 9 + 5 * 2 + 5 * numContentIds + 16 }
-  },
-  // assembles a section parser for the unmapped slice header, with slight
-  // variations depending on the major version of the cram file
-  cramMappedSliceHeader: function cramMappedSliceHeader(majorVersion) {
-    var parser = new Parser().itf8('refSeqId').itf8('refSeqStart').itf8('refSeqSpan').itf8('numRecords');
-    var maxLength = 5 * 4;
-
-    if (majorVersion >= 3) {
-      parser = parser.ltf8('recordCounter');
-      maxLength += 9;
-    } else if (majorVersion === 2) {
-      parser = parser.itf8('recordCounter');
-      maxLength += 5;
-    }
-
-    parser = parser.itf8('numBlocks').itf8('numContentIds').array('contentIds', {
-      type: singleItf8,
-      length: 'numContentIds'
-    }).itf8('refBaseBlockId');
-    maxLength += 5 * 3; // the md5 sum is missing in cram v1
-
-    if (majorVersion >= 2) {
-      parser = parser.array('md5', {
-        type: 'uint8',
-        length: 16
-      });
-      maxLength += 16;
-    }
-
-    var maxLengthFunc = function maxLengthFunc(numContentIds) {
-      return maxLength + numContentIds * 5;
-    };
-
-    return {
-      parser: parser,
-      maxLength: maxLengthFunc
-    };
-  },
-  cramEncoding: function cramEncoding(majorVersion) {
-    var parser = new Parser().namely('cramEncoding').itf8('codecId').itf8('parametersBytes').choice('parameters', {
-      tag: 'codecId',
-      choices: {
-        0: new Parser(),
-        // NULL
-        1: new Parser().itf8('blockContentId'),
-        // EXTERNAL
-        2: new Parser().itf8('offset').itf8('M'),
-        // GOLOMB,
-        // HUFFMAN_INT
-        3: Parser.start().itf8('numCodes').array('symbols', {
-          length: 'numCodes',
-          type: singleItf8
-        }).itf8('numLengths').array('bitLengths', {
-          length: 'numLengths',
-          type: singleItf8
-        }),
-        4: Parser.start() // BYTE_ARRAY_LEN
-        .nest('lengthsEncoding', {
-          type: 'cramEncoding'
-        }).nest('valuesEncoding', {
-          type: 'cramEncoding'
-        }),
-        // BYTE_ARRAY_STOP is a little different for CRAM v1
-        5: new Parser().uint8('stopByte')[majorVersion > 1 ? 'itf8' : 'int']('blockContentId'),
-        6: new Parser().itf8('offset').itf8('length'),
-        // BETA
-        7: new Parser().itf8('offset').itf8('K'),
-        // SUBEXP
-        8: new Parser().itf8('offset').itf8('log2m'),
-        // GOLOMB_RICE
-        9: new Parser().itf8('offset') // GAMMA
-
-      }
-    });
-    return {
-      parser: parser
-    };
-  },
-  cramDataSeriesEncodingMap: function cramDataSeriesEncodingMap(majorVersion) {
-    return new Parser().itf8('mapSize').itf8('mapCount').array('ents', {
-      length: 'mapCount',
-      type: new Parser().string('key', {
-        length: 2,
-        stripNull: false
-      }).nest('value', {
-        type: this.cramEncoding(majorVersion).parser
-      })
-    });
-  },
-  cramTagEncodingMap: function cramTagEncodingMap(majorVersion) {
-    return new Parser().itf8('mapSize').itf8('mapCount').array('ents', {
-      length: 'mapCount',
-      type: new Parser().itf8('key', {
-        formatter:
-        /* istanbul ignore next */
-        function formatter(integerRepresentation) {
-          return (
-            /* istanbul ignore next */
-            String.fromCharCode(integerRepresentation >> 16 & 0xff) + String.fromCharCode(integerRepresentation >> 8 & 0xff) + String.fromCharCode(integerRepresentation & 0xff)
-          );
+    // assemble a section parser for the unmapped slice header, with slight
+    // variations depending on the major version of the cram file
+    cramUnmappedSliceHeader: function (majorVersion) {
+        var maxLength = 0;
+        var parser = new binary_parser_1.Parser().itf8('numRecords');
+        maxLength += 5;
+        // recordCounter is itf8 in a CRAM v2 file, absent in CRAM v1
+        if (majorVersion >= 3) {
+            parser = parser.ltf8('recordCounter');
+            maxLength += 9;
         }
-      }).nest('value', {
-        type: this.cramEncoding(majorVersion).parser
-      })
-    });
-  },
-  cramCompressionHeader: function cramCompressionHeader(majorVersion) {
-    var parser = new Parser(); // TODO: if we want to support CRAM v1, we will need to refactor
-    // compression header into 2 parts to parse the landmarks,
-    // like the container header
-
-    parser = parser.nest('preservation', {
-      type: cramPreservationMap,
-      formatter: formatMap
-    }).nest('dataSeriesEncoding', {
-      type: this.cramDataSeriesEncodingMap(majorVersion),
-      formatter: formatMap
-    }).nest('tagEncoding', {
-      type: this.cramTagEncodingMap(majorVersion),
-      formatter: formatMap
-    });
-    return {
-      parser: parser
-    };
-  },
-  cramContainerHeader1: function cramContainerHeader1(majorVersion) {
-    var parser = new Parser().int32('length') // byte size of the container data (blocks)
-    .itf8('refSeqId') // reference sequence identifier, -1 for unmapped reads, -2 for multiple reference sequences
-    .itf8('refSeqStart') // the alignment start position or 0 for unmapped reads
-    .itf8('alignmentSpan') // the length of the alignment or 0 for unmapped reads
-    .itf8('numRecords'); // number of records in the container
-
-    var maxLength = 4 + 5 * 4;
-
-    if (majorVersion >= 3) {
-      parser = parser.ltf8('recordCounter'); // 1-based sequential index of records in the file/stream.
-
-      maxLength += 9;
-    } else if (majorVersion === 2) {
-      parser = parser.itf8('recordCounter');
-      maxLength += 5;
-    }
-
-    if (majorVersion > 1) {
-      parser = parser.ltf8('numBases'); // number of read bases
-
-      maxLength += 9;
-    }
-
-    parser = parser.itf8('numBlocks') // the number of blocks
-    .itf8('numLandmarks'); // the number of landmarks
-
-    maxLength += 5 + 5;
-    return {
-      parser: parser,
-      maxLength: maxLength
-    };
-  },
-  cramContainerHeader2: function cramContainerHeader2(majorVersion) {
-    var parser = new Parser().itf8('numLandmarks') // the number of blocks
-    // Each integer value of this array is a byte offset
-    // into the blocks byte array. Landmarks are used for
-    // random access indexing.
-    .array('landmarks', {
-      type: new Parser().itf8(),
-      length: 'numLandmarks'
-    });
-    var crcLength = 0;
-
-    if (majorVersion >= 3) {
-      parser = parser.uint32('crc32');
-      crcLength = 4;
-    }
-
-    return {
-      parser: parser,
-      maxLength: function maxLength(numLandmarks) {
-        return 5 + numLandmarks * 5 + crcLength;
-      }
-    };
-  }
+        else if (majorVersion === 2) {
+            parser = parser.itf8('recordCounter');
+            maxLength += 5;
+        }
+        parser = parser
+            .itf8('numBlocks')
+            .itf8('numContentIds')
+            .array('contentIds', {
+            type: singleItf8,
+            length: 'numContentIds',
+        });
+        maxLength += 5 * 2; // + numContentIds*5
+        // the md5 sum is missing in cram v1
+        if (majorVersion >= 2) {
+            parser = parser.array('md5', { type: 'uint8', length: 16 });
+            maxLength += 16;
+        }
+        var maxLengthFunc = function (numContentIds) { return maxLength + numContentIds * 5; };
+        return { parser: parser, maxLength: maxLengthFunc }; // : p, maxLength: numContentIds => 5 + 9 + 5 * 2 + 5 * numContentIds + 16 }
+    },
+    // assembles a section parser for the unmapped slice header, with slight
+    // variations depending on the major version of the cram file
+    cramMappedSliceHeader: function (majorVersion) {
+        var parser = new binary_parser_1.Parser()
+            .itf8('refSeqId')
+            .itf8('refSeqStart')
+            .itf8('refSeqSpan')
+            .itf8('numRecords');
+        var maxLength = 5 * 4;
+        if (majorVersion >= 3) {
+            parser = parser.ltf8('recordCounter');
+            maxLength += 9;
+        }
+        else if (majorVersion === 2) {
+            parser = parser.itf8('recordCounter');
+            maxLength += 5;
+        }
+        parser = parser
+            .itf8('numBlocks')
+            .itf8('numContentIds')
+            .array('contentIds', {
+            type: singleItf8,
+            length: 'numContentIds',
+        })
+            .itf8('refBaseBlockId');
+        maxLength += 5 * 3;
+        // the md5 sum is missing in cram v1
+        if (majorVersion >= 2) {
+            parser = parser.array('md5', { type: 'uint8', length: 16 });
+            maxLength += 16;
+        }
+        var maxLengthFunc = function (numContentIds) { return maxLength + numContentIds * 5; };
+        return { parser: parser, maxLength: maxLengthFunc };
+    },
+    cramEncoding: function (majorVersion) {
+        var parser = new binary_parser_1.Parser()
+            .namely('cramEncoding')
+            .itf8('codecId')
+            .itf8('parametersBytes')
+            .choice('parameters', {
+            tag: 'codecId',
+            choices: {
+                0: new binary_parser_1.Parser(),
+                1: new binary_parser_1.Parser().itf8('blockContentId'),
+                2: new binary_parser_1.Parser().itf8('offset').itf8('M'),
+                // HUFFMAN_INT
+                3: binary_parser_1.Parser.start()
+                    .itf8('numCodes')
+                    .array('symbols', { length: 'numCodes', type: singleItf8 })
+                    .itf8('numLengths')
+                    .array('bitLengths', { length: 'numLengths', type: singleItf8 }),
+                4: binary_parser_1.Parser.start() // BYTE_ARRAY_LEN
+                    .nest('lengthsEncoding', { type: 'cramEncoding' })
+                    .nest('valuesEncoding', { type: 'cramEncoding' }),
+                // BYTE_ARRAY_STOP is a little different for CRAM v1
+                5: new binary_parser_1.Parser()
+                    .uint8('stopByte')[majorVersion > 1 ? 'itf8' : 'int']('blockContentId'),
+                6: new binary_parser_1.Parser().itf8('offset').itf8('length'),
+                7: new binary_parser_1.Parser().itf8('offset').itf8('K'),
+                8: new binary_parser_1.Parser().itf8('offset').itf8('log2m'),
+                9: new binary_parser_1.Parser().itf8('offset'), // GAMMA
+            },
+        });
+        return { parser: parser };
+    },
+    cramDataSeriesEncodingMap: function (majorVersion) {
+        return new binary_parser_1.Parser()
+            .itf8('mapSize')
+            .itf8('mapCount')
+            .array('ents', {
+            length: 'mapCount',
+            type: new binary_parser_1.Parser()
+                .string('key', { length: 2, stripNull: false })
+                .nest('value', { type: this.cramEncoding(majorVersion).parser }),
+        });
+    },
+    cramTagEncodingMap: function (majorVersion) {
+        return new binary_parser_1.Parser()
+            .itf8('mapSize')
+            .itf8('mapCount')
+            .array('ents', {
+            length: 'mapCount',
+            type: new binary_parser_1.Parser()
+                .itf8('key', {
+                formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ integerRepresentation) {
+                    /* istanbul ignore next */
+                    return String.fromCharCode((integerRepresentation >> 16) & 0xff) +
+                        String.fromCharCode((integerRepresentation >> 8) & 0xff) +
+                        String.fromCharCode(integerRepresentation & 0xff);
+                },
+            })
+                .nest('value', { type: this.cramEncoding(majorVersion).parser }),
+        });
+    },
+    cramCompressionHeader: function (majorVersion) {
+        var parser = new binary_parser_1.Parser();
+        // TODO: if we want to support CRAM v1, we will need to refactor
+        // compression header into 2 parts to parse the landmarks,
+        // like the container header
+        parser = parser
+            .nest('preservation', {
+            type: cramPreservationMap,
+            formatter: formatMap,
+        })
+            .nest('dataSeriesEncoding', {
+            type: this.cramDataSeriesEncodingMap(majorVersion),
+            formatter: formatMap,
+        })
+            .nest('tagEncoding', {
+            type: this.cramTagEncodingMap(majorVersion),
+            formatter: formatMap,
+        });
+        return { parser: parser };
+    },
+    cramContainerHeader1: function (majorVersion) {
+        var parser = new binary_parser_1.Parser()
+            .int32('length') // byte size of the container data (blocks)
+            .itf8('refSeqId') // reference sequence identifier, -1 for unmapped reads, -2 for multiple reference sequences
+            .itf8('refSeqStart') // the alignment start position or 0 for unmapped reads
+            .itf8('alignmentSpan') // the length of the alignment or 0 for unmapped reads
+            .itf8('numRecords'); // number of records in the container
+        var maxLength = 4 + 5 * 4;
+        if (majorVersion >= 3) {
+            parser = parser.ltf8('recordCounter'); // 1-based sequential index of records in the file/stream.
+            maxLength += 9;
+        }
+        else if (majorVersion === 2) {
+            parser = parser.itf8('recordCounter');
+            maxLength += 5;
+        }
+        if (majorVersion > 1) {
+            parser = parser.ltf8('numBases'); // number of read bases
+            maxLength += 9;
+        }
+        parser = parser
+            .itf8('numBlocks') // the number of blocks
+            .itf8('numLandmarks'); // the number of landmarks
+        maxLength += 5 + 5;
+        return { parser: parser, maxLength: maxLength };
+    },
+    cramContainerHeader2: function (majorVersion) {
+        var parser = new binary_parser_1.Parser()
+            .itf8('numLandmarks') // the number of blocks
+            // Each integer value of this array is a byte offset
+            // into the blocks byte array. Landmarks are used for
+            // random access indexing.
+            .array('landmarks', {
+            type: new binary_parser_1.Parser().itf8(),
+            length: 'numLandmarks',
+        });
+        var crcLength = 0;
+        if (majorVersion >= 3) {
+            parser = parser.uint32('crc32');
+            crcLength = 4;
+        }
+        return {
+            parser: parser,
+            maxLength: function (numLandmarks) { return 5 + numLandmarks * 5 + crcLength; },
+        };
+    },
 };
-
 function getSectionParsers(majorVersion) {
-  var _context;
-
-  var parsers = (0, _assign.default)({}, unversionedParsers);
-  (0, _forEach.default)(_context = (0, _keys.default)(versionedParsers)).call(_context, function (parserName) {
-    parsers[parserName] = versionedParsers[parserName](majorVersion);
-  });
-  return parsers;
+    var parsers = Object.assign({}, unversionedParsers);
+    Object.keys(versionedParsers).forEach(function (parserName) {
+        parsers[parserName] = versionedParsers[parserName](majorVersion);
+    });
+    return parsers;
 }
-
-module.exports = {
-  cramFileDefinition: cramFileDefinition,
-  getSectionParsers: getSectionParsers
-};
+exports.getSectionParsers = getSectionParsers;
+//# sourceMappingURL=sectionParsers.js.map

dist/cramFile/slice/decodeRecord.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _isNan = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/number/is-nan"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _flags = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/flags"));
-
-var _slice = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/slice"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/toConsumableArray"));
-
-var _parseInt = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/number/parse-int"));
-
-var _minSafeInteger = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/number/min-safe-integer"));
-
-var _maxSafeInteger = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/number/max-safe-integer"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/slicedToArray"));
-
-var _indexOf = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/index-of"));
-
-var Long = require('long');
-
-var _require = require('../../errors'),
-    CramMalformedError = _require.CramMalformedError,
-    CramUnimplementedError = _require.CramUnimplementedError;
-
-var CramRecord = require('../record');
-
-var Constants = require('../constants');
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var long_1 = __importDefault(require("long"));
+var errors_1 = require("../../errors");
+var record_1 = __importDefault(require("../record"));
+var constants_1 = __importDefault(require("../constants"));
 /**
@@ -40,8 +14,8 @@ * given a Buffer, read a string up to the first null character
  */
-
-
 function readNullTerminatedStringFromBuffer(buffer) {
-  var zeroOffset = (0, _indexOf.default)(buffer).call(buffer, 0);
-  if (zeroOffset === -1) return buffer.toString('utf8');
-  return buffer.toString('utf8', 0, zeroOffset);
+    var zeroOffset = buffer.indexOf(0);
+    if (zeroOffset === -1) {
+        return buffer.toString('utf8');
+    }
+    return buffer.toString('utf8', 0, zeroOffset);
 }
@@ -52,278 +26,284 @@ /**
  */
-
-
 function parseTagValueArray(buffer) {
-  var arrayType = String.fromCharCode(buffer[0]);
-  var length = buffer.readInt32LE(1);
-  var schema = {
-    c: ['readInt8', 1],
-    C: ['readUInt8', 1],
-    s: ['readInt16LE', 2],
-    S: ['readUInt16LE', 2],
-    i: ['readInt32LE', 4],
-    I: ['readUInt32LE', 4],
-    f: ['readFloatLE', 4]
-  }[arrayType];
-  if (!schema) throw new CramMalformedError("invalid tag value array type '".concat(arrayType, "'"));
-
-  var _schema = (0, _slicedToArray2.default)(schema, 2),
-      getMethod = _schema[0],
-      itemSize = _schema[1];
-
-  var array = new Array(length);
-  var offset = 5;
-
-  for (var i = 0; i < length; i += 1) {
-    array[i] = buffer[getMethod](offset);
-    offset += itemSize;
-  }
-
-  return array;
+    var arrayType = String.fromCharCode(buffer[0]);
+    var length = buffer.readInt32LE(1);
+    var schema = {
+        c: ['readInt8', 1],
+        C: ['readUInt8', 1],
+        s: ['readInt16LE', 2],
+        S: ['readUInt16LE', 2],
+        i: ['readInt32LE', 4],
+        I: ['readUInt32LE', 4],
+        f: ['readFloatLE', 4],
+    }[arrayType];
+    if (!schema) {
+        throw new errors_1.CramMalformedError("invalid tag value array type '".concat(arrayType, "'"));
+    }
+    var getMethod = schema[0], itemSize = schema[1];
+    var array = new Array(length);
+    var offset = 5;
+    for (var i = 0; i < length; i += 1) {
+        array[i] = buffer[getMethod](offset);
+        offset += itemSize;
+    }
+    return array;
 }
-
 function parseTagData(tagType, buffer) {
-  if (!buffer.readInt32LE) buffer = Buffer.from(buffer);
-  if (tagType === 'Z') return readNullTerminatedStringFromBuffer(buffer);
-  if (tagType === 'A') return String.fromCharCode(buffer[0]);
-
-  if (tagType === 'I') {
-    var val = Long.fromBytesLE(buffer);
-    if (val.greaterThan(_maxSafeInteger.default) || val.lessThan(_minSafeInteger.default)) throw new CramUnimplementedError('integer overflow');
-    return val.toNumber();
-  }
-
-  if (tagType === 'i') return buffer.readInt32LE(0);
-  if (tagType === 's') return buffer.readInt16LE(0);
-  if (tagType === 'S') return buffer.readUInt16LE(0);
-  if (tagType === 'c') return buffer.readInt8(0);
-  if (tagType === 'C') return buffer.readUInt8(0);
-  if (tagType === 'f') return buffer.readFloatLE(0);
-
-  if (tagType === 'H') {
-    var hex = readNullTerminatedStringFromBuffer(buffer);
-    return (0, _parseInt.default)(hex.replace(/^0x/, ''), 16);
-  }
-
-  if (tagType === 'B') return parseTagValueArray(buffer);
-  throw new CramMalformedError("Unrecognized tag type ".concat(tagType));
+    if (!buffer.readInt32LE) {
+        buffer = Buffer.from(buffer);
+    }
+    if (tagType === 'Z') {
+        return readNullTerminatedStringFromBuffer(buffer);
+    }
+    if (tagType === 'A') {
+        return String.fromCharCode(buffer[0]);
+    }
+    if (tagType === 'I') {
+        var val = long_1.default.fromBytesLE(buffer);
+        if (val.greaterThan(Number.MAX_SAFE_INTEGER) ||
+            val.lessThan(Number.MIN_SAFE_INTEGER)) {
+            throw new errors_1.CramUnimplementedError('integer overflow');
+        }
+        return val.toNumber();
+    }
+    if (tagType === 'i') {
+        return buffer.readInt32LE(0);
+    }
+    if (tagType === 's') {
+        return buffer.readInt16LE(0);
+    }
+    if (tagType === 'S') {
+        return buffer.readUInt16LE(0);
+    }
+    if (tagType === 'c') {
+        return buffer.readInt8(0);
+    }
+    if (tagType === 'C') {
+        return buffer.readUInt8(0);
+    }
+    if (tagType === 'f') {
+        return buffer.readFloatLE(0);
+    }
+    if (tagType === 'H') {
+        var hex = readNullTerminatedStringFromBuffer(buffer);
+        return Number.parseInt(hex.replace(/^0x/, ''), 16);
+    }
+    if (tagType === 'B') {
+        return parseTagValueArray(buffer);
+    }
+    throw new errors_1.CramMalformedError("Unrecognized tag type ".concat(tagType));
 }
-
 function decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion) {
-  var currentReadPos = 0;
-  var currentRefPos = cramRecord.alignmentStart - 1;
-  var readFeatures = new Array(readFeatureCount);
-
-  function decodeRFData(_ref) {
-    var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-        type = _ref2[0],
-        dataSeriesName = _ref2[1];
-
-    var data = decodeDataSeries(dataSeriesName);
-
-    if (type === 'character') {
-      return String.fromCharCode(data);
+    var currentReadPos = 0;
+    var currentRefPos = cramRecord.alignmentStart - 1;
+    var readFeatures = new Array(readFeatureCount);
+    function decodeRFData(_a) {
+        var type = _a[0], dataSeriesName = _a[1];
+        var data = decodeDataSeries(dataSeriesName);
+        if (type === 'character') {
+            return String.fromCharCode(data);
+        }
+        if (type === 'string') {
+            return data.toString('utf8');
+        }
+        if (type === 'numArray') {
+            return data.toArray();
+        }
+        // else if (type === 'number') {
+        //   return data[0]
+        // }
+        return data;
     }
-
-    if (type === 'string') {
-      return data.toString('utf8');
+    for (var i = 0; i < readFeatureCount; i += 1) {
+        var code = String.fromCharCode(decodeDataSeries('FC'));
+        var readPosDelta = decodeDataSeries('FP');
+        var readFeature = { code: code };
+        // map of operator name -> data series name
+        var data1Schema = {
+            B: ['character', 'BA'],
+            S: ['string', majorVersion > 1 ? 'SC' : 'IN'],
+            X: ['number', 'BS'],
+            D: ['number', 'DL'],
+            I: ['string', 'IN'],
+            i: ['character', 'BA'],
+            b: ['string', 'BB'],
+            q: ['numArray', 'QQ'],
+            Q: ['number', 'QS'],
+            H: ['number', 'HC'],
+            P: ['number', 'PD'],
+            N: ['number', 'RS'],
+        }[code];
+        if (!data1Schema) {
+            throw new errors_1.CramMalformedError("invalid read feature code \"".concat(code, "\""));
+        }
+        readFeature.data = decodeRFData(data1Schema);
+        // if this is a tag with two data items, make the data an array and add the second item
+        var data2Schema = { B: ['number', 'QS'] }[code];
+        if (data2Schema) {
+            readFeature.data = [readFeature.data, decodeRFData(data2Schema)];
+        }
+        currentReadPos += readPosDelta;
+        readFeature.pos = currentReadPos;
+        currentRefPos += readPosDelta;
+        readFeature.refPos = currentRefPos;
+        // for gapping features, adjust the reference position for read features that follow
+        if (code === 'D' || code === 'N') {
+            currentRefPos += readFeature.data;
+        }
+        else if (code === 'I' || code === 'S') {
+            currentRefPos -= readFeature.data.length;
+        }
+        else if (code === 'i') {
+            currentRefPos -= 1;
+        }
+        readFeatures[i] = readFeature;
     }
-
-    if (type === 'numArray') {
-      return data.toArray();
-    } // else if (type === 'number') {
-    //   return data[0]
-    // }
-
-
-    return data;
-  }
-
-  for (var i = 0; i < readFeatureCount; i += 1) {
-    var code = String.fromCharCode(decodeDataSeries('FC'));
-    var readPosDelta = decodeDataSeries('FP');
-    var readFeature = {
-      code: code
-    }; // map of operator name -> data series name
-
-    var data1Schema = {
-      B: ['character', 'BA'],
-      S: ['string', majorVersion > 1 ? 'SC' : 'IN'],
-      // IN if cram v1, SC otherwise
-      X: ['number', 'BS'],
-      D: ['number', 'DL'],
-      I: ['string', 'IN'],
-      i: ['character', 'BA'],
-      b: ['string', 'BB'],
-      q: ['numArray', 'QQ'],
-      Q: ['number', 'QS'],
-      H: ['number', 'HC'],
-      P: ['number', 'PD'],
-      N: ['number', 'RS']
-    }[code];
-    if (!data1Schema) throw new CramMalformedError("invalid read feature code \"".concat(code, "\""));
-    readFeature.data = decodeRFData(data1Schema); // if this is a tag with two data items, make the data an array and add the second item
-
-    var data2Schema = {
-      B: ['number', 'QS']
-    }[code];
-    if (data2Schema) readFeature.data = [readFeature.data, decodeRFData(data2Schema)];
-    currentReadPos += readPosDelta;
-    readFeature.pos = currentReadPos;
-    currentRefPos += readPosDelta;
-    readFeature.refPos = currentRefPos; // for gapping features, adjust the reference position for read features that follow
-
-    if (code === 'D' || code === 'N') currentRefPos += readFeature.data;else if (code === 'I' || code === 'S') currentRefPos -= readFeature.data.length;else if (code === 'i') currentRefPos -= 1;
-    readFeatures[i] = readFeature;
-  }
-
-  return readFeatures;
+    return readFeatures;
 }
-
 function thingToString(thing) {
-  if (thing instanceof Buffer) {
-    return readNullTerminatedStringFromBuffer(thing);
-  }
-
-  if (thing.length && (0, _indexOf.default)(thing)) {
-    // array-like
-    if (!thing[thing.length - 1]) {
-      // trim zeroes off the end if necessary
-      var termIndex = (0, _indexOf.default)(thing).call(thing, 0);
-      return String.fromCharCode.apply(String, (0, _toConsumableArray2.default)((0, _slice.default)(thing).call(thing, 0, termIndex)));
+    if (thing instanceof Buffer) {
+        return readNullTerminatedStringFromBuffer(thing);
     }
-
-    return String.fromCharCode.apply(String, (0, _toConsumableArray2.default)(thing));
-  }
-
-  return String(thing);
+    if (thing.length && thing.indexOf) {
+        // array-like
+        if (!thing[thing.length - 1]) {
+            // trim zeroes off the end if necessary
+            var termIndex = thing.indexOf(0);
+            return String.fromCharCode.apply(String, thing.slice(0, termIndex));
+        }
+        return String.fromCharCode.apply(String, thing);
+    }
+    return String(thing);
 }
-
 function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber) {
-  var cramRecord = new CramRecord();
-  cramRecord.flags = decodeDataSeries('BF'); // note: the C data type of compressionFlags is byte in cram v1
-  // and int32 in cram v2+, but that does not matter for us here
-  // in javascript land.
-
-  cramRecord.cramFlags = decodeDataSeries('CF');
-  if (majorVersion > 1 && sliceHeader.content.refSeqId === -2) cramRecord.sequenceId = decodeDataSeries('RI');else cramRecord.sequenceId = sliceHeader.content.refSeqId;
-  cramRecord.readLength = decodeDataSeries('RL'); // if APDelta, will calculate the true start in a second pass
-
-  cramRecord.alignmentStart = decodeDataSeries('AP');
-  if (compressionScheme.APdelta) cramRecord.alignmentStart += cursors.lastAlignmentStart;
-  cursors.lastAlignmentStart = cramRecord.alignmentStart;
-  cramRecord.readGroupId = decodeDataSeries('RG');
-  if (compressionScheme.readNamesIncluded) cramRecord.readName = thingToString(decodeDataSeries('RN')); // mate record
-
-  if (cramRecord.isDetached()) {
-    // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
-    var mate = {};
-    mate.flags = decodeDataSeries('MF');
-
-    if (!compressionScheme.readNamesIncluded) {
-      mate.readName = thingToString(decodeDataSeries('RN'));
-      cramRecord.readName = mate.readName;
+    var cramRecord = new record_1.default();
+    cramRecord.flags = decodeDataSeries('BF');
+    // note: the C data type of compressionFlags is byte in cram v1
+    // and int32 in cram v2+, but that does not matter for us here
+    // in javascript land.
+    cramRecord.cramFlags = decodeDataSeries('CF');
+    if (majorVersion > 1 && sliceHeader.content.refSeqId === -2) {
+        cramRecord.sequenceId = decodeDataSeries('RI');
     }
-
-    mate.sequenceId = decodeDataSeries('NS');
-    mate.alignmentStart = decodeDataSeries('NP');
-    if ((0, _flags.default)(mate) || mate.sequenceId > -1) cramRecord.mate = mate;
-    cramRecord.templateSize = decodeDataSeries('TS'); // set mate unmapped if needed
-
-    if ((0, _flags.default)(mate) & Constants.CRAM_M_UNMAP) {
-      cramRecord.flags |= Constants.BAM_FMUNMAP;
-    } // set mate reversed if needed
-
-
-    if ((0, _flags.default)(mate) & Constants.CRAM_M_REVERSE) {
-      cramRecord.flags |= Constants.BAM_FMREVERSE;
-    } // detachedCount++
-
-  } else if (cramRecord.hasMateDownStream()) {
-    cramRecord.mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1;
-  } // TODO: the aux tag parsing will have to be refactored if we want to support
-  // cram v1
-
-
-  var TLindex = decodeDataSeries('TL');
-  if (TLindex < 0)
-    /* TODO: check nTL: TLindex >= compressionHeader.tagEncoding.size */
-    throw new CramMalformedError('invalid TL index'); // TN = tag names
-
-  var TN = compressionScheme.getTagNames(TLindex);
-  var ntags = TN.length;
-
-  for (var i = 0; i < ntags; i += 1) {
-    var tagId = TN[i];
-    var tagName = tagId.substr(0, 2);
-    var tagType = tagId.substr(2, 1);
-    var tagCodec = compressionScheme.getCodecForTag(tagId);
-    if (!tagCodec) throw new CramMalformedError("no codec defined for auxiliary tag ".concat(tagId));
-    var tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
-    cramRecord.tags[tagName] = parseTagData(tagType, tagData);
-  }
-
-  if (!cramRecord.isSegmentUnmapped()) {
-    var _context;
-
-    // reading read features
-    var
-    /* int */
-    readFeatureCount = decodeDataSeries('FN');
-
-    if (readFeatureCount) {
-      cramRecord.readFeatures = decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
-    } // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
-
-
-    var lengthOnRef = cramRecord.readLength;
-    if (cramRecord.readFeatures) (0, _forEach.default)(_context = cramRecord.readFeatures).call(_context, function (_ref3) {
-      var code = _ref3.code,
-          data = _ref3.data;
-      if (code === 'D' || code === 'N') lengthOnRef += data;else if (code === 'I' || code === 'S') lengthOnRef -= data.length;else if (code === 'i') lengthOnRef -= 1;
-    });
-
-    if ((0, _isNan.default)(lengthOnRef)) {
-      var _context2;
-
-      console.warn("".concat(cramRecord.readName || (0, _concat.default)(_context2 = "".concat(cramRecord.sequenceId, ":")).call(_context2, cramRecord.alignmentStart), " record has invalid read features"));
-      lengthOnRef = cramRecord.readLength;
+    else {
+        cramRecord.sequenceId = sliceHeader.content.refSeqId;
     }
-
-    cramRecord.lengthOnRef = lengthOnRef; // mapping quality
-
-    cramRecord.mappingQuality = decodeDataSeries('MQ');
-
-    if (cramRecord.isPreservingQualityScores()) {
-      var bases = new Array(cramRecord.readLength);
-
-      for (var _i = 0; _i < bases.length; _i += 1) {
-        bases[_i] = decodeDataSeries('QS');
-      }
-
-      cramRecord.qualityScores = bases;
+    cramRecord.readLength = decodeDataSeries('RL');
+    // if APDelta, will calculate the true start in a second pass
+    cramRecord.alignmentStart = decodeDataSeries('AP');
+    if (compressionScheme.APdelta) {
+        cramRecord.alignmentStart += cursors.lastAlignmentStart;
     }
-  } else if (cramRecord.isUnknownBases()) {
-    cramRecord.readBases = null;
-    cramRecord.qualityScores = null;
-  } else {
-    var _bases = new Array(cramRecord.readLength);
-
-    for (var _i2 = 0; _i2 < _bases.length; _i2 += 1) {
-      _bases[_i2] = decodeDataSeries('BA');
+    cursors.lastAlignmentStart = cramRecord.alignmentStart;
+    cramRecord.readGroupId = decodeDataSeries('RG');
+    if (compressionScheme.readNamesIncluded) {
+        cramRecord.readName = thingToString(decodeDataSeries('RN'));
     }
-
-    cramRecord.readBases = String.fromCharCode.apply(String, _bases);
-
-    if (cramRecord.isPreservingQualityScores()) {
-      for (var _i3 = 0; _i3 < _bases.length; _i3 += 1) {
-        _bases[_i3] = decodeDataSeries('QS');
-      }
-
-      cramRecord.qualityScores = _bases;
+    // mate record
+    if (cramRecord.isDetached()) {
+        // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
+        var mate = {};
+        mate.flags = decodeDataSeries('MF');
+        if (!compressionScheme.readNamesIncluded) {
+            mate.readName = thingToString(decodeDataSeries('RN'));
+            cramRecord.readName = mate.readName;
+        }
+        mate.sequenceId = decodeDataSeries('NS');
+        mate.alignmentStart = decodeDataSeries('NP');
+        if (mate.flags || mate.sequenceId > -1) {
+            cramRecord.mate = mate;
+        }
+        cramRecord.templateSize = decodeDataSeries('TS');
+        // set mate unmapped if needed
+        if (mate.flags & constants_1.default.CRAM_M_UNMAP) {
+            cramRecord.flags |= constants_1.default.BAM_FMUNMAP;
+        }
+        // set mate reversed if needed
+        if (mate.flags & constants_1.default.CRAM_M_REVERSE) {
+            cramRecord.flags |= constants_1.default.BAM_FMREVERSE;
+        }
+        // detachedCount++
     }
-  }
-
-  return cramRecord;
+    else if (cramRecord.hasMateDownStream()) {
+        cramRecord.mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1;
+    }
+    // TODO: the aux tag parsing will have to be refactored if we want to support
+    // cram v1
+    var TLindex = decodeDataSeries('TL');
+    if (TLindex < 0) {
+        /* TODO: check nTL: TLindex >= compressionHeader.tagEncoding.size */
+        throw new errors_1.CramMalformedError('invalid TL index');
+    }
+    // TN = tag names
+    var TN = compressionScheme.getTagNames(TLindex);
+    var ntags = TN.length;
+    for (var i = 0; i < ntags; i += 1) {
+        var tagId = TN[i];
+        var tagName = tagId.substr(0, 2);
+        var tagType = tagId.substr(2, 1);
+        var tagCodec = compressionScheme.getCodecForTag(tagId);
+        if (!tagCodec) {
+            throw new errors_1.CramMalformedError("no codec defined for auxiliary tag ".concat(tagId));
+        }
+        var tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+        cramRecord.tags[tagName] = parseTagData(tagType, tagData);
+    }
+    if (!cramRecord.isSegmentUnmapped()) {
+        // reading read features
+        var /* int */ readFeatureCount = decodeDataSeries('FN');
+        if (readFeatureCount) {
+            cramRecord.readFeatures = decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
+        }
+        // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
+        var lengthOnRef_1 = cramRecord.readLength;
+        if (cramRecord.readFeatures) {
+            cramRecord.readFeatures.forEach(function (_a) {
+                var code = _a.code, data = _a.data;
+                if (code === 'D' || code === 'N') {
+                    lengthOnRef_1 += data;
+                }
+                else if (code === 'I' || code === 'S') {
+                    lengthOnRef_1 -= data.length;
+                }
+                else if (code === 'i') {
+                    lengthOnRef_1 -= 1;
+                }
+            });
+        }
+        if (Number.isNaN(lengthOnRef_1)) {
+            console.warn("".concat(cramRecord.readName ||
+                "".concat(cramRecord.sequenceId, ":").concat(cramRecord.alignmentStart), " record has invalid read features"));
+            lengthOnRef_1 = cramRecord.readLength;
+        }
+        cramRecord.lengthOnRef = lengthOnRef_1;
+        // mapping quality
+        cramRecord.mappingQuality = decodeDataSeries('MQ');
+        if (cramRecord.isPreservingQualityScores()) {
+            var bases = new Array(cramRecord.readLength);
+            for (var i = 0; i < bases.length; i += 1) {
+                bases[i] = decodeDataSeries('QS');
+            }
+            cramRecord.qualityScores = bases;
+        }
+    }
+    else if (cramRecord.isUnknownBases()) {
+        cramRecord.readBases = null;
+        cramRecord.qualityScores = null;
+    }
+    else {
+        var bases = new Array(cramRecord.readLength);
+        for (var i = 0; i < bases.length; i += 1) {
+            bases[i] = decodeDataSeries('BA');
+        }
+        cramRecord.readBases = String.fromCharCode.apply(String, bases);
+        if (cramRecord.isPreservingQualityScores()) {
+            for (var i = 0; i < bases.length; i += 1) {
+                bases[i] = decodeDataSeries('QS');
+            }
+            cramRecord.qualityScores = bases;
+        }
+    }
+    return cramRecord;
 }
-
-module.exports = decodeRecord;
+exports.default = decodeRecord;
+//# sourceMappingURL=decodeRecord.js.map

dist/cramFile/slice/index.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _values = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/values"));
-
-var _promise = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/promise"));
-
-var _filter = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/filter"));
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _flags = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/flags"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _map = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/map"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/toConsumableArray"));
-
-var _context17;
-
-var _require = require('../../errors'),
-    CramMalformedError = _require.CramMalformedError,
-    CramBufferOverrunError = _require.CramBufferOverrunError,
-    CramArgumentError = _require.CramArgumentError;
-
-var _require2 = require('../util'),
-    parseItem = _require2.parseItem,
-    tinyMemoize = _require2.tinyMemoize,
-    sequenceMD5 = _require2.sequenceMD5;
-
-var Constants = require('../constants');
-
-var decodeRecord = require('./decodeRecord');
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+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 util_1 = require("../util");
+var constants_1 = __importDefault(require("../constants"));
+var decodeRecord_1 = __importDefault(require("./decodeRecord"));
 /**
@@ -51,29 +53,26 @@ * @private
  */
-
-
 function calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumber, thisRecord) {
-  function getAllMatedRecords(startRecord) {
-    var records = [startRecord];
-
-    if (startRecord.mateRecordNumber >= 0) {
-      var mateRecord = allRecords[startRecord.mateRecordNumber];
-      if (!mateRecord) throw new CramMalformedError('intra-slice mate record not found, this file seems malformed');
-      records.push.apply(records, (0, _toConsumableArray2.default)(getAllMatedRecords(mateRecord)));
+    function getAllMatedRecords(startRecord) {
+        var records = [startRecord];
+        if (startRecord.mateRecordNumber >= 0) {
+            var mateRecord = allRecords[startRecord.mateRecordNumber];
+            if (!mateRecord) {
+                throw new errors_1.CramMalformedError('intra-slice mate record not found, this file seems malformed');
+            }
+            records.push.apply(records, getAllMatedRecords(mateRecord));
+        }
+        return records;
     }
-
-    return records;
-  }
-
-  var matedRecords = getAllMatedRecords(thisRecord);
-  var starts = (0, _map.default)(matedRecords).call(matedRecords, function (r) {
-    return r.alignmentStart;
-  });
-  var ends = (0, _map.default)(matedRecords).call(matedRecords, function (r) {
-    return r.alignmentStart + r.readLength - 1;
-  });
-  var estimatedTemplateLength = Math.max.apply(Math, (0, _toConsumableArray2.default)(ends)) - Math.min.apply(Math, (0, _toConsumableArray2.default)(starts)) + 1;
-  if (estimatedTemplateLength >= 0) (0, _forEach.default)(matedRecords).call(matedRecords, function (r) {
-    if (r.templateLength !== undefined) throw new CramMalformedError('mate pair group has some members that have template lengths already, this file seems malformed');
-    r.templateLength = estimatedTemplateLength;
-  });
+    var matedRecords = getAllMatedRecords(thisRecord);
+    var starts = matedRecords.map(function (r) { return r.alignmentStart; });
+    var ends = matedRecords.map(function (r) { return r.alignmentStart + r.readLength - 1; });
+    var estimatedTemplateLength = Math.max.apply(Math, ends) - Math.min.apply(Math, starts) + 1;
+    if (estimatedTemplateLength >= 0) {
+        matedRecords.forEach(function (r) {
+            if (r.templateLength !== undefined) {
+                throw new errors_1.CramMalformedError('mate pair group has some members that have template lengths already, this file seems malformed');
+            }
+            r.templateLength = estimatedTemplateLength;
+        });
+    }
 }
@@ -87,12 +86,10 @@ /**
  */
-
-
 function calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord) {
-  // this just estimates the template length by using the simple (non-gapped) end coordinate of each
-  // read, because gapping in the alignment doesn't mean the template is longer or shorter
-  var start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart);
-  var end = Math.max(thisRecord.alignmentStart + thisRecord.readLength - 1, mateRecord.alignmentStart + mateRecord.readLength - 1);
-  var lengthEstimate = end - start + 1;
-  thisRecord.templateLength = lengthEstimate;
-  mateRecord.templateLength = lengthEstimate;
+    // this just estimates the template length by using the simple (non-gapped) end coordinate of each
+    // read, because gapping in the alignment doesn't mean the template is longer or shorter
+    var start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart);
+    var end = Math.max(thisRecord.alignmentStart + thisRecord.readLength - 1, mateRecord.alignmentStart + mateRecord.readLength - 1);
+    var lengthEstimate = end - start + 1;
+    thisRecord.templateLength = lengthEstimate;
+    mateRecord.templateLength = lengthEstimate;
 }
@@ -104,728 +101,430 @@ /**
  */
-
-
 function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, mateRecord) {
-  if (!mateRecord) throw new CramMalformedError('could not resolve intra-slice mate pairs, file seems truncated or malformed');
-  var complicatedMultiSegment = !!(mateRecord.mate || mateRecord.mateRecordNumber !== undefined && mateRecord.mateRecordNumber !== currentRecordNumber); // Deal with lossy read names
-
-  if (!thisRecord.readName) {
-    thisRecord.readName = String(thisRecord.uniqueId);
-    mateRecord.readName = thisRecord.readName;
-  }
-
-  thisRecord.mate = {
-    sequenceId: mateRecord.sequenceId,
-    alignmentStart: mateRecord.alignmentStart,
-    uniqueId: mateRecord.uniqueId
-  };
-  if (mateRecord.readName) thisRecord.mate.readName = mateRecord.readName; // the mate record might have its own mate pointer, if this is some kind of
-  // multi-segment (more than paired) scheme, so only relate that one back to this one
-  // if it does not have any other relationship
-
-  if (!mateRecord.mate && mateRecord.mateRecordNumber === undefined) {
-    mateRecord.mate = {
-      sequenceId: thisRecord.sequenceId,
-      alignmentStart: thisRecord.alignmentStart,
-      uniqueId: thisRecord.uniqueId
+    if (!mateRecord) {
+        throw new errors_1.CramMalformedError('could not resolve intra-slice mate pairs, file seems truncated or malformed');
+    }
+    var complicatedMultiSegment = !!(mateRecord.mate ||
+        (mateRecord.mateRecordNumber !== undefined &&
+            mateRecord.mateRecordNumber !== currentRecordNumber));
+    // Deal with lossy read names
+    if (!thisRecord.readName) {
+        thisRecord.readName = String(thisRecord.uniqueId);
+        mateRecord.readName = thisRecord.readName;
+    }
+    thisRecord.mate = {
+        sequenceId: mateRecord.sequenceId,
+        alignmentStart: mateRecord.alignmentStart,
+        uniqueId: mateRecord.uniqueId,
     };
-    if (thisRecord.readName) mateRecord.mate.readName = thisRecord.readName;
-  } // make sure the proper flags and cramFlags are set on both records
-  // paired
-
-
-  thisRecord.flags |= Constants.BAM_FPAIRED; // set mate unmapped if needed
-
-  if ((0, _flags.default)(mateRecord) & Constants.BAM_FUNMAP) {
-    thisRecord.flags |= Constants.BAM_FMUNMAP; // thisRecord.templateLength = 0
-  }
-
-  if ((0, _flags.default)(thisRecord) & Constants.BAM_FUNMAP) {
-    // thisRecord.templateLength = 0
-    mateRecord.flags |= Constants.BAM_FMUNMAP;
-  } // set mate reversed if needed
-
-
-  if ((0, _flags.default)(mateRecord) & Constants.BAM_FREVERSE) {
-    thisRecord.flags |= Constants.BAM_FMREVERSE;
-  }
-
-  if ((0, _flags.default)(thisRecord) & Constants.BAM_FREVERSE) {
-    mateRecord.flags |= Constants.BAM_FMREVERSE;
-  }
-
-  if (thisRecord.templateLength === undefined) {
-    if (complicatedMultiSegment) calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumber, thisRecord);else calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord);
-  } // delete this last because it's used by the
-  // complicated template length estimation
-
-
-  delete thisRecord.mateRecordNumber;
+    if (mateRecord.readName) {
+        thisRecord.mate.readName = mateRecord.readName;
+    }
+    // the mate record might have its own mate pointer, if this is some kind of
+    // multi-segment (more than paired) scheme, so only relate that one back to this one
+    // if it does not have any other relationship
+    if (!mateRecord.mate && mateRecord.mateRecordNumber === undefined) {
+        mateRecord.mate = {
+            sequenceId: thisRecord.sequenceId,
+            alignmentStart: thisRecord.alignmentStart,
+            uniqueId: thisRecord.uniqueId,
+        };
+        if (thisRecord.readName) {
+            mateRecord.mate.readName = thisRecord.readName;
+        }
+    }
+    // make sure the proper flags and cramFlags are set on both records
+    // paired
+    thisRecord.flags |= constants_1.default.BAM_FPAIRED;
+    // set mate unmapped if needed
+    if (mateRecord.flags & constants_1.default.BAM_FUNMAP) {
+        thisRecord.flags |= constants_1.default.BAM_FMUNMAP;
+        // thisRecord.templateLength = 0
+    }
+    if (thisRecord.flags & constants_1.default.BAM_FUNMAP) {
+        // thisRecord.templateLength = 0
+        mateRecord.flags |= constants_1.default.BAM_FMUNMAP;
+    }
+    // set mate reversed if needed
+    if (mateRecord.flags & constants_1.default.BAM_FREVERSE) {
+        thisRecord.flags |= constants_1.default.BAM_FMREVERSE;
+    }
+    if (thisRecord.flags & constants_1.default.BAM_FREVERSE) {
+        mateRecord.flags |= constants_1.default.BAM_FMREVERSE;
+    }
+    if (thisRecord.templateLength === undefined) {
+        if (complicatedMultiSegment) {
+            calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumber, thisRecord);
+        }
+        else {
+            calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord);
+        }
+    }
+    // delete this last because it's used by the
+    // complicated template length estimation
+    delete thisRecord.mateRecordNumber;
 }
-
-var CramSlice =
-/*#__PURE__*/
-function () {
-  function CramSlice(container, position) {
-    (0, _classCallCheck2.default)(this, CramSlice);
-    this.container = container;
-    this.file = container.file;
-    this.containerPosition = position;
-  } // memoize
-
-
-  (0, _createClass2.default)(CramSlice, [{
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee() {
-        var sectionParsers, containerHeader, header;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.file.getSectionParsers();
-
-              case 2:
-                sectionParsers = _context.sent;
-                _context.next = 5;
-                return this.container.getHeader();
-
-              case 5:
-                containerHeader = _context.sent;
-                _context.next = 8;
-                return this.file.readBlock(containerHeader._endPosition + this.containerPosition);
-
-              case 8:
-                header = _context.sent;
-
-                if (!(header.contentType === 'MAPPED_SLICE_HEADER')) {
-                  _context.next = 13;
-                  break;
-                }
-
-                header.content = parseItem(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
-                _context.next = 18;
-                break;
-
-              case 13:
-                if (!(header.contentType === 'UNMAPPED_SLICE_HEADER')) {
-                  _context.next = 17;
-                  break;
-                }
-
-                header.content = parseItem(header.content, sectionParsers.cramUnmappedSliceHeader.parser, 0, containerHeader._endPosition);
-                _context.next = 18;
-                break;
-
-              case 17:
-                throw new CramMalformedError("error reading slice header block, invalid content type ".concat(header._contentType));
-
-              case 18:
-                return _context.abrupt("return", header);
-
-              case 19:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getHeader() {
-        return _getHeader.apply(this, arguments);
-      }
-
-      return getHeader;
-    }() // memoize
-
-  }, {
-    key: "getBlocks",
-    value: function () {
-      var _getBlocks = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee2() {
-        var header, blockPosition, blocks, i;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.getHeader();
-
-              case 2:
-                header = _context2.sent;
-                // read all the blocks into memory and store them
-                blockPosition = header._endPosition;
-                blocks = new Array(header.content.numBlocks);
-                i = 0;
-
-              case 6:
-                if (!(i < blocks.length)) {
-                  _context2.next = 14;
-                  break;
-                }
-
-                _context2.next = 9;
-                return this.file.readBlock(blockPosition);
-
-              case 9:
-                blocks[i] = _context2.sent;
-                blockPosition = blocks[i]._endPosition;
-
-              case 11:
-                i += 1;
-                _context2.next = 6;
-                break;
-
-              case 14:
-                return _context2.abrupt("return", blocks);
-
-              case 15:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getBlocks() {
-        return _getBlocks.apply(this, arguments);
-      }
-
-      return getBlocks;
-    }() // no memoize
-
-  }, {
-    key: "getCoreDataBlock",
-    value: function () {
-      var _getCoreDataBlock = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee3() {
-        var blocks;
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return this.getBlocks();
-
-              case 2:
-                blocks = _context3.sent;
-                return _context3.abrupt("return", blocks[0]);
-
-              case 4:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getCoreDataBlock() {
-        return _getCoreDataBlock.apply(this, arguments);
-      }
-
-      return getCoreDataBlock;
-    }() // memoize
-
-  }, {
-    key: "_getBlocksContentIdIndex",
-    value: function () {
-      var _getBlocksContentIdIndex2 = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee4() {
-        var blocks, blocksByContentId;
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.getBlocks();
-
-              case 2:
-                blocks = _context4.sent;
-                blocksByContentId = {};
-                (0, _forEach.default)(blocks).call(blocks, function (block) {
-                  if (block.contentType === 'EXTERNAL_DATA') {
-                    blocksByContentId[block.contentId] = block;
-                  }
-                });
-                return _context4.abrupt("return", blocksByContentId);
-
-              case 6:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function _getBlocksContentIdIndex() {
-        return _getBlocksContentIdIndex2.apply(this, arguments);
-      }
-
-      return _getBlocksContentIdIndex;
-    }()
-  }, {
-    key: "getBlockByContentId",
-    value: function () {
-      var _getBlockByContentId = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee5(id) {
-        var blocksByContentId;
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
-                _context5.next = 2;
-                return this._getBlocksContentIdIndex();
-
-              case 2:
-                blocksByContentId = _context5.sent;
-                return _context5.abrupt("return", blocksByContentId[id]);
-
-              case 4:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function getBlockByContentId(_x) {
-        return _getBlockByContentId.apply(this, arguments);
-      }
-
-      return getBlockByContentId;
-    }()
-  }, {
-    key: "getReferenceRegion",
-    value: function () {
-      var _getReferenceRegion = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee6() {
-        var sliceHeader, compressionScheme, refBlock, seq;
-        return _regenerator.default.wrap(function _callee6$(_context6) {
-          while (1) {
-            switch (_context6.prev = _context6.next) {
-              case 0:
-                _context6.next = 2;
-                return this.getHeader();
-
-              case 2:
-                sliceHeader = _context6.sent.content;
-
-                if (!(sliceHeader.refSeqId < 0)) {
-                  _context6.next = 5;
-                  break;
-                }
-
-                return _context6.abrupt("return", undefined);
-
-              case 5:
-                _context6.next = 7;
-                return this.container.getCompressionScheme();
-
-              case 7:
-                compressionScheme = _context6.sent;
-
-                if (!(sliceHeader.refBaseBlockId >= 0)) {
-                  _context6.next = 15;
-                  break;
-                }
-
-                refBlock = this.getBlockByContentId(sliceHeader.refBaseBlockId);
-
-                if (refBlock) {
-                  _context6.next = 12;
-                  break;
-                }
-
-                throw new CramMalformedError('embedded reference specified, but reference block does not exist');
-
-              case 12:
-                if (!(sliceHeader.span > refBlock.uncompressedSize)) {
-                  _context6.next = 14;
-                  break;
-                }
-
-                throw new CramMalformedError('Embedded reference is too small');
-
-              case 14:
-                return _context6.abrupt("return", {
-                  seq: refBlock.data.toString('utf8'),
-                  start: sliceHeader.refSeqStart,
-                  end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
-                  span: sliceHeader.refSeqSpan
-                });
-
-              case 15:
-                if (!(compressionScheme.referenceRequired || this.file.fetchReferenceSequenceCallback)) {
-                  _context6.next = 24;
-                  break;
-                }
-
-                if (this.file.fetchReferenceSequenceCallback) {
-                  _context6.next = 18;
-                  break;
-                }
-
-                throw new Error('reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence');
-
-              case 18:
-                _context6.next = 20;
-                return this.file.fetchReferenceSequenceCallback(sliceHeader.refSeqId, sliceHeader.refSeqStart, sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1);
-
-              case 20:
-                seq = _context6.sent;
-
-                if (!(seq.length !== sliceHeader.refSeqSpan)) {
-                  _context6.next = 23;
-                  break;
-                }
-
-                throw new CramArgumentError('seqFetch callback returned a reference sequence of the wrong length');
-
-              case 23:
-                return _context6.abrupt("return", {
-                  seq: seq,
-                  start: sliceHeader.refSeqStart,
-                  end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
-                  span: sliceHeader.refSeqSpan
-                });
-
-              case 24:
-                return _context6.abrupt("return", undefined);
-
-              case 25:
-              case "end":
-                return _context6.stop();
-            }
-          }
-        }, _callee6, this);
-      }));
-
-      function getReferenceRegion() {
-        return _getReferenceRegion.apply(this, arguments);
-      }
-
-      return getReferenceRegion;
-    }()
-  }, {
-    key: "getAllRecords",
-    value: function getAllRecords() {
-      return this.getRecords(function () {
-        return true;
-      });
+var CramSlice = /** @class */ (function () {
+    function CramSlice(container, position) {
+        this.container = container;
+        this.file = container.file;
+        this.containerPosition = position;
     }
-  }, {
-    key: "_fetchRecords",
-    value: function () {
-      var _fetchRecords2 = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee7() {
-        var _this = this;
-
-        var _ref, majorVersion, compressionScheme, sliceHeader, blocksByContentId, refRegion, _context7, _context8, _context9, _context10, _context11, seq, start, end, seqMd5, storedMd5, coreDataBlock, cursors, decodeDataSeries, records, i, _i, mateRecordNumber;
-
-        return _regenerator.default.wrap(function _callee7$(_context12) {
-          while (1) {
-            switch (_context12.prev = _context12.next) {
-              case 0:
-                _context12.next = 2;
-                return this.file.getDefinition();
-
-              case 2:
-                _ref = _context12.sent;
-                majorVersion = _ref.majorVersion;
-                _context12.next = 6;
-                return this.container.getCompressionScheme();
-
-              case 6:
-                compressionScheme = _context12.sent;
-                _context12.next = 9;
-                return this.getHeader();
-
-              case 9:
-                sliceHeader = _context12.sent;
-                _context12.next = 12;
-                return this._getBlocksContentIdIndex();
-
-              case 12:
-                blocksByContentId = _context12.sent;
-
-                if (!(majorVersion > 1 && this.file.options.checkSequenceMD5 && sliceHeader.content.refSeqId >= 0 && sliceHeader.content.md5.join('') !== '0000000000000000')) {
-                  _context12.next = 23;
-                  break;
+    // memoize
+    CramSlice.prototype.getHeader = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var sectionParsers, containerHeader, header;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.file.getSectionParsers()];
+                    case 1:
+                        sectionParsers = _a.sent();
+                        return [4 /*yield*/, this.container.getHeader()];
+                    case 2:
+                        containerHeader = _a.sent();
+                        return [4 /*yield*/, this.file.readBlock(containerHeader._endPosition + this.containerPosition)];
+                    case 3:
+                        header = _a.sent();
+                        if (header.contentType === 'MAPPED_SLICE_HEADER') {
+                            header.content = (0, util_1.parseItem)(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
+                        }
+                        else if (header.contentType === 'UNMAPPED_SLICE_HEADER') {
+                            header.content = (0, util_1.parseItem)(header.content, sectionParsers.cramUnmappedSliceHeader.parser, 0, containerHeader._endPosition);
+                        }
+                        else {
+                            throw new errors_1.CramMalformedError("error reading slice header block, invalid content type ".concat(header._contentType));
+                        }
+                        return [2 /*return*/, header];
                 }
-
-                _context12.next = 16;
-                return this.getReferenceRegion();
-
-              case 16:
-                refRegion = _context12.sent;
-
-                if (!refRegion) {
-                  _context12.next = 23;
-                  break;
+            });
+        });
+    };
+    // memoize
+    CramSlice.prototype.getBlocks = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var header, blockPosition, blocks, i, _a, _b;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0: return [4 /*yield*/, this.getHeader()
+                        // read all the blocks into memory and store them
+                    ];
+                    case 1:
+                        header = _c.sent();
+                        blockPosition = header._endPosition;
+                        blocks = new Array(header.content.numBlocks);
+                        i = 0;
+                        _c.label = 2;
+                    case 2:
+                        if (!(i < blocks.length)) return [3 /*break*/, 5];
+                        _a = blocks;
+                        _b = i;
+                        return [4 /*yield*/, this.file.readBlock(blockPosition)];
+                    case 3:
+                        _a[_b] = _c.sent();
+                        blockPosition = blocks[i]._endPosition;
+                        _c.label = 4;
+                    case 4:
+                        i += 1;
+                        return [3 /*break*/, 2];
+                    case 5: return [2 /*return*/, blocks];
                 }
-
-                seq = refRegion.seq, start = refRegion.start, end = refRegion.end;
-                seqMd5 = sequenceMD5(seq);
-                storedMd5 = (0, _map.default)(_context7 = sliceHeader.content.md5).call(_context7, function (byte) {
-                  return (byte < 16 ? '0' : '') + byte.toString(16);
-                }).join('');
-
-                if (!(seqMd5 !== storedMd5)) {
-                  _context12.next = 23;
-                  break;
+            });
+        });
+    };
+    // no memoize
+    CramSlice.prototype.getCoreDataBlock = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var blocks;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getBlocks()
+                        // the core data block is always the first block in the slice
+                    ];
+                    case 1:
+                        blocks = _a.sent();
+                        // the core data block is always the first block in the slice
+                        return [2 /*return*/, blocks[0]];
                 }
-
-                throw new CramMalformedError((0, _concat.default)(_context8 = (0, _concat.default)(_context9 = (0, _concat.default)(_context10 = (0, _concat.default)(_context11 = "MD5 checksum reference mismatch for ref ".concat(sliceHeader.content.refSeqId, " pos ")).call(_context11, start, "..")).call(_context10, end, ". recorded MD5: ")).call(_context9, storedMd5, ", calculated MD5: ")).call(_context8, seqMd5));
-
-              case 23:
-                _context12.next = 25;
-                return this.getCoreDataBlock();
-
-              case 25:
-                coreDataBlock = _context12.sent;
-                cursors = {
-                  lastAlignmentStart: sliceHeader.content.refSeqStart || 0,
-                  coreBlock: {
-                    bitPosition: 7,
-                    bytePosition: 0
-                  },
-                  externalBlocks: {
-                    getCursor: function getCursor(contentId) {
-                      if (!this[contentId]) this[contentId] = {
-                        bitPosition: 7,
-                        bytePosition: 0
-                      };
-                      return this[contentId];
-                    }
-                  }
-                };
-
-                decodeDataSeries = function decodeDataSeries(dataSeriesName) {
-                  var codec = compressionScheme.getCodecForDataSeries(dataSeriesName);
-                  if (!codec) throw new CramMalformedError("no codec defined for ".concat(dataSeriesName, " data series")); // console.log(dataSeriesName, Object.getPrototypeOf(codec))
-
-                  return codec.decode(_this, coreDataBlock, blocksByContentId, cursors);
-                };
-
-                records = new Array(sliceHeader.content.numRecords);
-                i = 0;
-
-              case 30:
-                if (!(i < records.length)) {
-                  _context12.next = 48;
-                  break;
+            });
+        });
+    };
+    // memoize
+    CramSlice.prototype._getBlocksContentIdIndex = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var blocks, blocksByContentId;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getBlocks()];
+                    case 1:
+                        blocks = _a.sent();
+                        blocksByContentId = {};
+                        blocks.forEach(function (block) {
+                            if (block.contentType === 'EXTERNAL_DATA') {
+                                blocksByContentId[block.contentId] = block;
+                            }
+                        });
+                        return [2 /*return*/, blocksByContentId];
                 }
-
-                _context12.prev = 31;
-                records[i] = decodeRecord(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
-                records[i].uniqueId = sliceHeader.contentPosition + sliceHeader.content.recordCounter + i + 1;
-                _context12.next = 45;
-                break;
-
-              case 36:
-                _context12.prev = 36;
-                _context12.t0 = _context12["catch"](31);
-
-                if (!(_context12.t0 instanceof CramBufferOverrunError)) {
-                  _context12.next = 44;
-                  break;
+            });
+        });
+    };
+    CramSlice.prototype.getBlockByContentId = function (id) {
+        return __awaiter(this, void 0, void 0, function () {
+            var blocksByContentId;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this._getBlocksContentIdIndex()];
+                    case 1:
+                        blocksByContentId = _a.sent();
+                        return [2 /*return*/, blocksByContentId[id]];
                 }
-
-                console.warn('read attempted beyond end of buffer, file seems truncated.');
-                records = (0, _filter.default)(records).call(records, function (r) {
-                  return !!r;
-                });
-                return _context12.abrupt("break", 48);
-
-              case 44:
-                throw _context12.t0;
-
-              case 45:
-                i += 1;
-                _context12.next = 30;
-                break;
-
-              case 48:
-                // interpret `recordsToNextFragment` attributes to make standard `mate` objects
-                // Resolve mate pair cross-references between records in this slice
-                for (_i = 0; _i < records.length; _i += 1) {
-                  mateRecordNumber = records[_i].mateRecordNumber;
-                  if (mateRecordNumber >= 0) associateIntraSliceMate(records, _i, records[_i], records[mateRecordNumber]);
+            });
+        });
+    };
+    CramSlice.prototype.getReferenceRegion = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var sliceHeader, compressionScheme, refBlock, seq;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getHeader()];
+                    case 1:
+                        sliceHeader = (_a.sent()).content;
+                        if (sliceHeader.refSeqId < 0) {
+                            return [2 /*return*/, undefined];
+                        }
+                        return [4 /*yield*/, this.container.getCompressionScheme()
+                            // console.log(JSON.stringify(sliceHeader, null, '  '))
+                        ];
+                    case 2:
+                        compressionScheme = _a.sent();
+                        // console.log(JSON.stringify(sliceHeader, null, '  '))
+                        if (sliceHeader.refBaseBlockId >= 0) {
+                            refBlock = this.getBlockByContentId(sliceHeader.refBaseBlockId);
+                            if (!refBlock) {
+                                throw new errors_1.CramMalformedError('embedded reference specified, but reference block does not exist');
+                            }
+                            if (sliceHeader.span > refBlock.uncompressedSize) {
+                                throw new errors_1.CramMalformedError('Embedded reference is too small');
+                            }
+                            return [2 /*return*/, {
+                                    seq: refBlock.data.toString('utf8'),
+                                    start: sliceHeader.refSeqStart,
+                                    end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
+                                    span: sliceHeader.refSeqSpan,
+                                }];
+                        }
+                        if (!(compressionScheme.referenceRequired ||
+                            this.file.fetchReferenceSequenceCallback)) return [3 /*break*/, 4];
+                        if (!this.file.fetchReferenceSequenceCallback) {
+                            throw new Error('reference sequence not embedded, and seqFetch callback not provided, cannot fetch reference sequence');
+                        }
+                        return [4 /*yield*/, this.file.fetchReferenceSequenceCallback(sliceHeader.refSeqId, sliceHeader.refSeqStart, sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1)];
+                    case 3:
+                        seq = _a.sent();
+                        if (seq.length !== sliceHeader.refSeqSpan) {
+                            throw new errors_1.CramArgumentError('seqFetch callback returned a reference sequence of the wrong length');
+                        }
+                        return [2 /*return*/, {
+                                seq: seq,
+                                start: sliceHeader.refSeqStart,
+                                end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
+                                span: sliceHeader.refSeqSpan,
+                            }];
+                    case 4: return [2 /*return*/, undefined];
                 }
-
-                return _context12.abrupt("return", records);
-
-              case 50:
-              case "end":
-                return _context12.stop();
-            }
-          }
-        }, _callee7, this, [[31, 36]]);
-      }));
-
-      function _fetchRecords() {
-        return _fetchRecords2.apply(this, arguments);
-      }
-
-      return _fetchRecords;
-    }()
-  }, {
-    key: "getRecords",
-    value: function () {
-      var _getRecords = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee9(filterFunction) {
-        var _context13,
-            _this2 = this;
-
-        var cacheKey, recordsPromise, records, sliceHeader, _context14, singleRefId, _compressionScheme, refRegions, i, seqId, refRegion, end, _i2, _seqId, _refRegion;
-
-        return _regenerator.default.wrap(function _callee9$(_context16) {
-          while (1) {
-            switch (_context16.prev = _context16.next) {
-              case 0:
-                // fetch the features if necessary, using the file-level feature cache
-                cacheKey = this.container.filePosition + this.containerPosition;
-                recordsPromise = this.file.featureCache.get(cacheKey);
-
-                if (!recordsPromise) {
-                  recordsPromise = this._fetchRecords();
-                  this.file.featureCache.set(cacheKey, recordsPromise);
+            });
+        });
+    };
+    CramSlice.prototype.getAllRecords = function () {
+        return this.getRecords(function () { return true; });
+    };
+    CramSlice.prototype._fetchRecords = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var majorVersion, compressionScheme, sliceHeader, blocksByContentId, refRegion, seq, start, end, seqMd5, storedMd5, coreDataBlock, cursors, decodeDataSeries, records, i, i, mateRecordNumber;
+            var _this = this;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.file.getDefinition()];
+                    case 1:
+                        majorVersion = (_a.sent()).majorVersion;
+                        return [4 /*yield*/, this.container.getCompressionScheme()];
+                    case 2:
+                        compressionScheme = _a.sent();
+                        return [4 /*yield*/, this.getHeader()];
+                    case 3:
+                        sliceHeader = _a.sent();
+                        return [4 /*yield*/, this._getBlocksContentIdIndex()
+                            // check MD5 of reference if available
+                        ];
+                    case 4:
+                        blocksByContentId = _a.sent();
+                        if (!(majorVersion > 1 &&
+                            this.file.options.checkSequenceMD5 &&
+                            sliceHeader.content.refSeqId >= 0 &&
+                            sliceHeader.content.md5.join('') !== '0000000000000000')) return [3 /*break*/, 6];
+                        return [4 /*yield*/, this.getReferenceRegion()];
+                    case 5:
+                        refRegion = _a.sent();
+                        if (refRegion) {
+                            seq = refRegion.seq, start = refRegion.start, end = refRegion.end;
+                            seqMd5 = (0, util_1.sequenceMD5)(seq);
+                            storedMd5 = sliceHeader.content.md5
+                                .map(function (byte) { return (byte < 16 ? '0' : '') + byte.toString(16); })
+                                .join('');
+                            if (seqMd5 !== storedMd5) {
+                                throw new errors_1.CramMalformedError("MD5 checksum reference mismatch for ref ".concat(sliceHeader.content.refSeqId, " pos ").concat(start, "..").concat(end, ". recorded MD5: ").concat(storedMd5, ", calculated MD5: ").concat(seqMd5));
+                            }
+                        }
+                        _a.label = 6;
+                    case 6: return [4 /*yield*/, this.getCoreDataBlock()];
+                    case 7:
+                        coreDataBlock = _a.sent();
+                        cursors = {
+                            lastAlignmentStart: sliceHeader.content.refSeqStart || 0,
+                            coreBlock: { bitPosition: 7, bytePosition: 0 },
+                            externalBlocks: {
+                                getCursor: function (contentId) {
+                                    if (!this[contentId]) {
+                                        this[contentId] = { bitPosition: 7, bytePosition: 0 };
+                                    }
+                                    return this[contentId];
+                                },
+                            },
+                        };
+                        decodeDataSeries = function (dataSeriesName) {
+                            var codec = compressionScheme.getCodecForDataSeries(dataSeriesName);
+                            if (!codec) {
+                                throw new errors_1.CramMalformedError("no codec defined for ".concat(dataSeriesName, " data series"));
+                            }
+                            // console.log(dataSeriesName, Object.getPrototypeOf(codec))
+                            return codec.decode(_this, coreDataBlock, blocksByContentId, cursors);
+                        };
+                        records = new Array(sliceHeader.content.numRecords);
+                        for (i = 0; i < records.length; i += 1) {
+                            try {
+                                records[i] = (0, decodeRecord_1.default)(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
+                                records[i].uniqueId =
+                                    sliceHeader.contentPosition +
+                                        sliceHeader.content.recordCounter +
+                                        i +
+                                        1;
+                            }
+                            catch (e) {
+                                if (e instanceof errors_1.CramBufferOverrunError) {
+                                    console.warn('read attempted beyond end of buffer, file seems truncated.');
+                                    records = records.filter(function (r) { return !!r; });
+                                    break;
+                                }
+                                else {
+                                    throw e;
+                                }
+                            }
+                        }
+                        // interpret `recordsToNextFragment` attributes to make standard `mate` objects
+                        // Resolve mate pair cross-references between records in this slice
+                        for (i = 0; i < records.length; i += 1) {
+                            mateRecordNumber = records[i].mateRecordNumber;
+                            if (mateRecordNumber >= 0) {
+                                associateIntraSliceMate(records, i, records[i], records[mateRecordNumber]);
+                            }
+                        }
+                        return [2 /*return*/, records];
                 }
-
-                _context16.t0 = _filter.default;
-                _context16.next = 6;
-                return recordsPromise;
-
-              case 6:
-                _context16.t1 = _context13 = _context16.sent;
-                _context16.t2 = _context13;
-                _context16.t3 = filterFunction;
-                records = (0, _context16.t0)(_context16.t1).call(_context16.t2, _context16.t3);
-
-                if (!(records.length && this.file.fetchReferenceSequenceCallback)) {
-                  _context16.next = 24;
-                  break;
-                }
-
-                _context16.next = 13;
-                return this.getHeader();
-
-              case 13:
-                sliceHeader = _context16.sent;
-
-                if (!(sliceHeader.content.refSeqId >= 0 || // single-ref slice
-                sliceHeader.content.refSeqId === -2 // multi-ref slice
-                )) {
-                  _context16.next = 24;
-                  break;
-                }
-
-                singleRefId = sliceHeader.content.refSeqId >= 0 ? sliceHeader.content.refSeqId : undefined;
-                _context16.next = 18;
-                return this.container.getCompressionScheme();
-
-              case 18:
-                _compressionScheme = _context16.sent;
-                refRegions = {}; // seqId => { start, end, seq }
-                // iterate over the records to find the spans of the reference sequences we need to fetch
-
-                for (i = 0; i < records.length; i += 1) {
-                  seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
-                  refRegion = refRegions[seqId];
-
-                  if (!refRegion) {
-                    refRegion = {
-                      id: seqId,
-                      start: records[i].alignmentStart,
-                      end: -Infinity
-                    };
-                    refRegions[seqId] = refRegion;
-                  }
-
-                  end = records[i].alignmentStart + (records[i].lengthOnRef || records[i].readLength) - 1;
-                  if (end > refRegion.end) refRegion.end = end;
-                  if (records[i].alignmentStart < refRegion.start) refRegion.start = records[i].alignmentStart;
-                } // fetch the `seq` for all of the ref regions
-
-
-                _context16.next = 23;
-                return _promise.default.all((0, _map.default)(_context14 = (0, _values.default)(refRegions)).call(_context14,
-                /*#__PURE__*/
-                function () {
-                  var _ref2 = (0, _asyncToGenerator2.default)(
-                  /*#__PURE__*/
-                  _regenerator.default.mark(function _callee8(refRegion) {
-                    return _regenerator.default.wrap(function _callee8$(_context15) {
-                      while (1) {
-                        switch (_context15.prev = _context15.next) {
-                          case 0:
-                            if (!(refRegion.id !== -1 && refRegion.start <= refRegion.end)) {
-                              _context15.next = 4;
-                              break;
+            });
+        });
+    };
+    CramSlice.prototype.getRecords = function (filterFunction) {
+        return __awaiter(this, void 0, void 0, function () {
+            var cacheKey, recordsPromise, records, sliceHeader, singleRefId, compressionScheme, refRegions, i, seqId, refRegion, end, i, seqId, refRegion;
+            var _this = this;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        cacheKey = this.container.filePosition + this.containerPosition;
+                        recordsPromise = this.file.featureCache.get(cacheKey);
+                        if (!recordsPromise) {
+                            recordsPromise = this._fetchRecords();
+                            this.file.featureCache.set(cacheKey, recordsPromise);
+                        }
+                        return [4 /*yield*/, recordsPromise];
+                    case 1:
+                        records = (_a.sent()).filter(filterFunction);
+                        if (!(records.length && this.file.fetchReferenceSequenceCallback)) return [3 /*break*/, 5];
+                        return [4 /*yield*/, this.getHeader()];
+                    case 2:
+                        sliceHeader = _a.sent();
+                        if (!(sliceHeader.content.refSeqId >= 0 || // single-ref slice
+                            sliceHeader.content.refSeqId === -2) // multi-ref slice
+                        ) return [3 /*break*/, 5]; // multi-ref slice
+                        singleRefId = sliceHeader.content.refSeqId >= 0
+                            ? sliceHeader.content.refSeqId
+                            : undefined;
+                        return [4 /*yield*/, this.container.getCompressionScheme()];
+                    case 3:
+                        compressionScheme = _a.sent();
+                        refRegions = {} // seqId => { start, end, seq }
+                        ;
+                        // iterate over the records to find the spans of the reference sequences we need to fetch
+                        for (i = 0; i < records.length; i += 1) {
+                            seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
+                            refRegion = refRegions[seqId];
+                            if (!refRegion) {
+                                refRegion = {
+                                    id: seqId,
+                                    start: records[i].alignmentStart,
+                                    end: -Infinity,
+                                };
+                                refRegions[seqId] = refRegion;
                             }
-
-                            _context15.next = 3;
-                            return _this2.file.fetchReferenceSequenceCallback(refRegion.id, refRegion.start, refRegion.end);
-
-                          case 3:
-                            refRegion.seq = _context15.sent;
-
-                          case 4:
-                          case "end":
-                            return _context15.stop();
+                            end = records[i].alignmentStart +
+                                (records[i].lengthOnRef || records[i].readLength) -
+                                1;
+                            if (end > refRegion.end) {
+                                refRegion.end = end;
+                            }
+                            if (records[i].alignmentStart < refRegion.start) {
+                                refRegion.start = records[i].alignmentStart;
+                            }
                         }
-                      }
-                    }, _callee8);
-                  }));
-
-                  return function (_x3) {
-                    return _ref2.apply(this, arguments);
-                  };
-                }()));
-
-              case 23:
-                // now decorate all the records with them
-                for (_i2 = 0; _i2 < records.length; _i2 += 1) {
-                  _seqId = singleRefId !== undefined ? singleRefId : records[_i2].sequenceId;
-                  _refRegion = refRegions[_seqId];
-
-                  if (_refRegion && _refRegion.seq) {
-                    records[_i2].addReferenceSequence(_refRegion, _compressionScheme);
-                  }
+                        // fetch the `seq` for all of the ref regions
+                        return [4 /*yield*/, Promise.all(Object.values(refRegions).map(function (refRegion) { return __awaiter(_this, void 0, void 0, function () {
+                                var _a;
+                                return __generator(this, function (_b) {
+                                    switch (_b.label) {
+                                        case 0:
+                                            if (!(refRegion.id !== -1 && refRegion.start <= refRegion.end)) return [3 /*break*/, 2];
+                                            _a = refRegion;
+                                            return [4 /*yield*/, this.file.fetchReferenceSequenceCallback(refRegion.id, refRegion.start, refRegion.end)];
+                                        case 1:
+                                            _a.seq = _b.sent();
+                                            _b.label = 2;
+                                        case 2: return [2 /*return*/];
+                                    }
+                                });
+                            }); }))
+                            // now decorate all the records with them
+                        ];
+                    case 4:
+                        // fetch the `seq` for all of the ref regions
+                        _a.sent();
+                        // now decorate all the records with them
+                        for (i = 0; i < records.length; i += 1) {
+                            seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
+                            refRegion = refRegions[seqId];
+                            if (refRegion && refRegion.seq) {
+                                records[i].addReferenceSequence(refRegion, compressionScheme);
+                            }
+                        }
+                        _a.label = 5;
+                    case 5: return [2 /*return*/, records];
                 }
-
-              case 24:
-                return _context16.abrupt("return", records);
-
-              case 25:
-              case "end":
-                return _context16.stop();
-            }
-          }
-        }, _callee9, this);
-      }));
-
-      function getRecords(_x2) {
-        return _getRecords.apply(this, arguments);
-      }
-
-      return getRecords;
-    }()
-  }]);
-  return CramSlice;
-}(); // memoize several methods in the class for performance
-
-
-(0, _forEach.default)(_context17 = 'getHeader getBlocks _getBlocksContentIdIndex'.split(' ')).call(_context17, function (method) {
-  return tinyMemoize(CramSlice, method);
-});
-module.exports = CramSlice;
+            });
+        });
+    };
+    return CramSlice;
+}());
+exports.default = CramSlice;
+// memoize several methods in the class for performance
+'getHeader getBlocks _getBlocksContentIdIndex'
+    .split(' ')
+    .forEach(function (method) { return (0, util_1.tinyMemoize)(CramSlice, method); });
+//# sourceMappingURL=index.js.map

dist/cramFile/util.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _promise = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/promise"));
-
-var md5 = require('md5');
-
-var _require = require('../errors'),
-    CramBufferOverrunError = _require.CramBufferOverrunError;
-
-module.exports = {
-  itf8Size: function itf8Size(v) {
-    if (!(v & ~0x7f)) return 1;
-    if (!(v & ~0x3fff)) return 2;
-    if (!(v & ~0x1fffff)) return 3;
-    if (!(v & ~0xfffffff)) return 4;
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.sequenceMD5 = exports.tinyMemoize = exports.parseItem = exports.parseItf8 = exports.itf8Size = void 0;
+var md5_1 = __importDefault(require("md5"));
+var errors_1 = require("../errors");
+function itf8Size(v) {
+    if (!(v & ~0x7f)) {
+        return 1;
+    }
+    if (!(v & ~0x3fff)) {
+        return 2;
+    }
+    if (!(v & ~0x1fffff)) {
+        return 3;
+    }
+    if (!(v & ~0xfffffff)) {
+        return 4;
+    }
     return 5;
-  },
-  parseItf8: function parseItf8(buffer, initialOffset) {
+}
+exports.itf8Size = itf8Size;
+function parseItf8(buffer, initialOffset) {
     var offset = initialOffset;
     var countFlags = buffer[offset];
     var result;
-
     if (countFlags < 0x80) {
-      result = countFlags;
-      offset += 1;
-    } else if (countFlags < 0xc0) {
-      result = (countFlags << 8 | buffer[offset + 1]) & 0x3fff;
-      offset += 2;
-    } else if (countFlags < 0xe0) {
-      result = (countFlags << 16 | buffer[offset + 1] << 8 | buffer[offset + 2]) & 0x1fffff;
-      offset += 3;
-    } else if (countFlags < 0xf0) {
-      result = (countFlags << 24 | buffer[offset + 1] << 16 | buffer[offset + 2] << 8 | buffer[offset + 3]) & 0x0fffffff;
-      offset += 4;
-    } else {
-      result = (countFlags & 0x0f) << 28 | 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);
-      // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
-
-      offset += 5;
+        result = countFlags;
+        offset += 1;
     }
-
+    else if (countFlags < 0xc0) {
+        result = ((countFlags << 8) | buffer[offset + 1]) & 0x3fff;
+        offset += 2;
+    }
+    else if (countFlags < 0xe0) {
+        result =
+            ((countFlags << 16) | (buffer[offset + 1] << 8) | buffer[offset + 2]) &
+                0x1fffff;
+        offset += 3;
+    }
+    else if (countFlags < 0xf0) {
+        result =
+            ((countFlags << 24) |
+                (buffer[offset + 1] << 16) |
+                (buffer[offset + 2] << 8) |
+                buffer[offset + 3]) &
+                0x0fffffff;
+        offset += 4;
+    }
+    else {
+        result =
+            ((countFlags & 0x0f) << 28) |
+                (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);
+        // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
+        offset += 5;
+    }
     if (offset > buffer.length) {
-      throw new CramBufferOverrunError('Attempted to read beyond end of buffer; this file seems truncated.');
+        throw new errors_1.CramBufferOverrunError('Attempted to read beyond end of buffer; this file seems truncated.');
     }
-
     return [result, offset - initialOffset];
-  },
-  // parseLtf8(buffer, initialOffset) {
-  //   let offset = initialOffset
-  //   const countFlags = buffer[offset]
-  //   let result
-  //   if (countFlags < 0x80) {
-  //     result = countFlags
-  //     offset += 1
-  //   } else if (countFlags < 0xc0) {
-  //     result = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff
-  //     offset += 2
-  //   } else if (countFlags < 0xe0) {
-  //     result =
-  //       ((buffer[offset] << 16) |
-  //         (buffer[offset + 1] << 8) |
-  //         buffer[offset + 2]) &
-  //       0x1fffff
-  //     offset += 3
-  //   } else if (countFlags < 0xf0) {
-  //     result =
-  //       ((buffer[offset] << 24) |
-  //         (buffer[offset + 1] << 16) |
-  //         (buffer[offset + 2] << 8) |
-  //         buffer[offset + 3]) &
-  //       0x0fffffff
-  //     offset += 4
-  //   } else if (countFlags < 0xf8) {
-  //     result =
-  //       ((buffer[offset] & 15) * Math.pow(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;
-  //     offset += 5
-  //   } else if (countFlags < 0xfc) {
-  //     result =
-  //       ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2,32) +
-  //         (buffer[offset + 2] << 24)) |
-  //       ((buffer[offset + 3] << 16) |
-  //         (buffer[offset + 4] << 8) |
-  //         buffer[offset + 5])
-  //     offset += 6
-  //   } else if (countFlags < 0xfe) {
-  //     result =
-  //       ((((buffer[offset] & 3) << 16) |
-  //         (buffer[offset + 1] << 8) |
-  //         buffer[offset + 2]) *
-  //         Math.pow(2,32) +
-  //         (buffer[offset + 3] << 24)) |
-  //       ((buffer[offset + 4] << 16) |
-  //         (buffer[offset + 5] << 8) |
-  //         buffer[offset + 6])
-  //     offset += 7
-  //   } else if (countFlags < 0xff) {
-  //     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 8))
-  //     if (
-  //       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
-  //       result.lessThan(Number.MIN_SAFE_INTEGER)
-  //     )
-  //       throw new CramUnimplementedError('integer overflow')
-  //     result = result.toNumber()
-  //     offset += 8
-  //   } else {
-  //     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 9))
-  //     if (
-  //       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
-  //       result.lessThan(Number.MIN_SAFE_INTEGER)
-  //     )
-  //       throw new CramUnimplementedError('integer overflow')
-  //     result = result.toNumber()
-  //     offset += 9
-  //   }
-  //   return [result, offset - initialOffset]
-  // },
-  parseItem: function parseItem(buffer, parser) {
-    var startBufferPosition = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : 0;
-    var startFilePosition = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : 0;
-
-    var _parser$parse = parser.parse(buffer),
-        offset = _parser$parse.offset,
-        result = _parser$parse.result;
-
+}
+exports.parseItf8 = parseItf8;
+// parseLtf8(buffer, initialOffset) {
+//   let offset = initialOffset
+//   const countFlags = buffer[offset]
+//   let result
+//   if (countFlags < 0x80) {
+//     result = countFlags
+//     offset += 1
+//   } else if (countFlags < 0xc0) {
+//     result = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff
+//     offset += 2
+//   } else if (countFlags < 0xe0) {
+//     result =
+//       ((buffer[offset] << 16) |
+//         (buffer[offset + 1] << 8) |
+//         buffer[offset + 2]) &
+//       0x1fffff
+//     offset += 3
+//   } else if (countFlags < 0xf0) {
+//     result =
+//       ((buffer[offset] << 24) |
+//         (buffer[offset + 1] << 16) |
+//         (buffer[offset + 2] << 8) |
+//         buffer[offset + 3]) &
+//       0x0fffffff
+//     offset += 4
+//   } else if (countFlags < 0xf8) {
+//     result =
+//       ((buffer[offset] & 15) * Math.pow(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;
+//     offset += 5
+//   } else if (countFlags < 0xfc) {
+//     result =
+//       ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2,32) +
+//         (buffer[offset + 2] << 24)) |
+//       ((buffer[offset + 3] << 16) |
+//         (buffer[offset + 4] << 8) |
+//         buffer[offset + 5])
+//     offset += 6
+//   } else if (countFlags < 0xfe) {
+//     result =
+//       ((((buffer[offset] & 3) << 16) |
+//         (buffer[offset + 1] << 8) |
+//         buffer[offset + 2]) *
+//         Math.pow(2,32) +
+//         (buffer[offset + 3] << 24)) |
+//       ((buffer[offset + 4] << 16) |
+//         (buffer[offset + 5] << 8) |
+//         buffer[offset + 6])
+//     offset += 7
+//   } else if (countFlags < 0xff) {
+//     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 8))
+//     if (
+//       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
+//       result.lessThan(Number.MIN_SAFE_INTEGER)
+//     )
+//       throw new CramUnimplementedError('integer overflow')
+//     result = result.toNumber()
+//     offset += 8
+//   } else {
+//     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 9))
+//     if (
+//       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
+//       result.lessThan(Number.MIN_SAFE_INTEGER)
+//     )
+//       throw new CramUnimplementedError('integer overflow')
+//     result = result.toNumber()
+//     offset += 9
+//   }
+//   return [result, offset - initialOffset]
+// },
+function parseItem(buffer, parser, startBufferPosition, startFilePosition) {
+    if (startBufferPosition === void 0) { startBufferPosition = 0; }
+    if (startFilePosition === void 0) { startFilePosition = 0; }
+    var _a = parser.parse(buffer), offset = _a.offset, result = _a.result;
     result._endPosition = offset + startFilePosition;
     result._size = offset - startBufferPosition;
     return result;
-  },
-  // this would be nice as a decorator, but i'm a little worried about
-  // babel support for it going away or changing.
-  // memoizes a method in the stupidest possible way, with no regard for the
-  // arguments.  actually, this only works on methods that take no arguments
-  tinyMemoize: function tinyMemoize(_class, methodName) {
+}
+exports.parseItem = parseItem;
+// this would be nice as a decorator, but i'm a little worried about
+// babel support for it going away or changing.
+// memoizes a method in the stupidest possible way, with no regard for the
+// arguments.  actually, this only works on methods that take no arguments
+function tinyMemoize(_class, methodName) {
     var method = _class.prototype[methodName];
     var memoAttrName = "_memo_".concat(methodName);
-
     _class.prototype[methodName] = function _tinyMemoized() {
-      var _this = this;
-
-      if (!(memoAttrName in this)) {
-        var res = method.call(this);
-        this[memoAttrName] = res;
-
-        _promise.default.resolve(res).catch(function () {
-          delete _this[memoAttrName];
-        });
-      }
-
-      return this[memoAttrName];
+        var _this = this;
+        if (!(memoAttrName in this)) {
+            var res = method.call(this);
+            this[memoAttrName] = res;
+            Promise.resolve(res).catch(function () {
+                delete _this[memoAttrName];
+            });
+        }
+        return this[memoAttrName];
     };
-  },
-  sequenceMD5: function sequenceMD5(seq) {
-    return md5(seq.toUpperCase().replace(/[^\x21-\x7e]/g, ''));
-  }
-};
+}
+exports.tinyMemoize = tinyMemoize;
+function sequenceMD5(seq) {
+    return (0, md5_1.default)(seq.toUpperCase().replace(/[^\x21-\x7e]/g, ''));
+}
+exports.sequenceMD5 = sequenceMD5;
+//# sourceMappingURL=util.js.map

dist/errors.js

 "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

dist/index.js

 "use strict";
-
-var CramFile = require('./cramFile');
-
-var IndexedCramFile = require('./indexedCramFile');
-
-var CraiIndex = require('./craiIndex');
-
-module.exports = {
-  CramFile: CramFile,
-  IndexedCramFile: IndexedCramFile,
-  CraiIndex: CraiIndex
-};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.CraiIndex = exports.IndexedCramFile = exports.CramFile = void 0;
+var cramFile_1 = __importDefault(require("./cramFile"));
+exports.CramFile = cramFile_1.default;
+var indexedCramFile_1 = __importDefault(require("./indexedCramFile"));
+exports.IndexedCramFile = indexedCramFile_1.default;
+var craiIndex_1 = __importDefault(require("./craiIndex"));
+exports.CraiIndex = craiIndex_1.default;
+//# sourceMappingURL=index.js.map

dist/indexedCramFile.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _sort = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/sort"));
-
-var _filter = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/filter"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/slicedToArray"));
-
-var _entries = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/entries"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/toConsumableArray"));
-
-var _promise = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/promise"));
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _map = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/map"));
-
-var _reduce = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/reduce"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _require = require('./errors'),
-    CramUnimplementedError = _require.CramUnimplementedError,
-    CramSizeLimitError = _require.CramSizeLimitError;
-
-var CramFile = require('./cramFile');
-
-var IndexedCramFile =
-/*#__PURE__*/
-function () {
-  /**
-   *
-   * @param {object} args
-   * @param {CramFile} args.cram
-   * @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
-   * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
-   * @param {number} [args.fetchSizeLimit] optional maximum number of bytes to fetch in a single getRecordsForRange call.  Default 3 MiB.
-   * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
-   * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
-   */
-  function IndexedCramFile(args) {
-    (0, _classCallCheck2.default)(this, IndexedCramFile);
-    // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
-    if (args.cram) this.cram = args.cram;else this.cram = new CramFile({
-      url: args.cramUrl,
-      path: args.cramPath,
-      filehandle: args.cramFilehandle,
-      seqFetch: args.seqFetch,
-      checkSequenceMD5: args.checkSequenceMD5,
-      cacheSize: args.cacheSize
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
-    if (!(this.cram instanceof CramFile)) throw new Error('invalid arguments: no cramfile');
-    this.index = args.index;
-    if (!this.index.getEntriesForRange) throw new Error('invalid arguments: not an index');
-    this.fetchSizeLimit = args.fetchSizeLimit || 3000000;
-  }
-  /**
-   *
-   * @param {number} seq numeric ID of the reference sequence
-   * @param {number} start start of the range of interest. 1-based closed coordinates.
-   * @param {number} end end of the range of interest. 1-based closed coordinates.
-   * @returns {Promise[Array[CramRecord]]}
-   */
-
-
-  (0, _createClass2.default)(IndexedCramFile, [{
-    key: "getRecordsForRange",
-    value: function () {
-      var _getRecordsForRange = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee(seq, start, end) {
-        var _context,
-            _context2,
-            _this = this,
-            _context3,
-            _concatInstanceProper,
-            _context4;
-
-        var opts,
-            seqId,
-            slices,
-            totalSize,
-            filter,
-            sliceResults,
-            ret,
-            _context5,
-            _context6,
-            _context7,
-            readNames,
-            readIds,
-            i,
-            name,
-            id,
-            unmatedPairs,
-            matePromises,
-            _i,
-            _name,
-            mateSlices,
-            mateBlocks,
-            mateChunks,
-            _i2,
-            _mateChunks,
-            mateRecordPromises,
-            mateFeatPromises,
-            mateTotalSize,
-            _context8,
-            newMateFeats,
-            newMates,
-            _args = arguments;
-
-        return _regenerator.default.wrap(function _callee$(_context9) {
-          while (1) {
-            switch (_context9.prev = _context9.next) {
-              case 0:
-                opts = _args.length > 3 && _args[3] !== undefined ? _args[3] : {};
-                opts.viewAsPairs = opts.viewAsPairs || false;
-                opts.pairAcrossChr = opts.pairAcrossChr || false;
-                opts.maxInsertSize = opts.maxInsertSize || 200000;
-
-                if (!(typeof seq === 'string')) {
-                  _context9.next = 6;
-                  break;
-                }
-
-                throw new CramUnimplementedError('string sequence names not yet supported');
-
-              case 6:
-                seqId = seq;
-                _context9.next = 9;
-                return this.index.getEntriesForRange(seqId, start, end);
-
-              case 9:
-                slices = _context9.sent;
-                totalSize = (0, _reduce.default)(_context = (0, _map.default)(slices).call(slices, function (s) {
-                  return s.sliceBytes;
-                })).call(_context, function (a, b) {
-                  return a + b;
-                }, 0);
-
-                if (!(totalSize > this.fetchSizeLimit)) {
-                  _context9.next = 13;
-                  break;
-                }
-
-                throw new CramSizeLimitError((0, _concat.default)(_context2 = "data size of ".concat(totalSize.toLocaleString(), " bytes exceeded fetch size limit of ")).call(_context2, this.fetchSizeLimit.toLocaleString(), " bytes"));
-
-              case 13:
-                // TODO: do we need to merge or de-duplicate the blocks?
-                // fetch all the slices and parse the feature data
-                filter = function filter(feature) {
-                  return feature.sequenceId === seq && feature.alignmentStart <= end && feature.alignmentStart + feature.lengthOnRef - 1 >= start;
-                };
-
-                _context9.next = 16;
-                return _promise.default.all((0, _map.default)(slices).call(slices, function (slice) {
-                  return _this.getRecordsInSlice(slice, filter);
-                }));
-
-              case 16:
-                sliceResults = _context9.sent;
-                ret = (_concatInstanceProper = (0, _concat.default)(_context3 = Array.prototype)).call.apply(_concatInstanceProper, (0, _concat.default)(_context4 = [_context3]).call(_context4, (0, _toConsumableArray2.default)(sliceResults)));
-
-                if (!opts.viewAsPairs) {
-                  _context9.next = 42;
-                  break;
-                }
-
-                readNames = {};
-                readIds = {};
-
-                for (i = 0; i < ret.length; i += 1) {
-                  name = ret[i].readName;
-                  id = ret[i].uniqueId;
-                  if (!readNames[name]) readNames[name] = 0;
-                  readNames[name] += 1;
-                  readIds[id] = 1;
-                }
-
-                unmatedPairs = {};
-                (0, _forEach.default)(_context5 = (0, _entries.default)(readNames)).call(_context5, function (_ref) {
-                  var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-                      k = _ref2[0],
-                      v = _ref2[1];
-
-                  if (v === 1) unmatedPairs[k] = true;
-                });
-                matePromises = [];
-
-                for (_i = 0; _i < ret.length; _i += 1) {
-                  _name = ret[_i].readName;
-
-                  if (unmatedPairs[_name] && ret[_i].mate && (ret[_i].mate.sequenceId === seqId || opts.pairAcrossChr) && Math.abs(ret[_i].alignmentStart - ret[_i].mate.alignmentStart) < opts.maxInsertSize) {
-                    mateSlices = this.index.getEntriesForRange(ret[_i].mate.sequenceId, ret[_i].mate.alignmentStart, ret[_i].mate.alignmentStart + 1);
-                    matePromises.push(mateSlices);
-                  }
-                }
-
-                _context9.next = 28;
-                return _promise.default.all(matePromises);
-
-              case 28:
-                mateBlocks = _context9.sent;
-                mateChunks = [];
-
-                for (_i2 = 0; _i2 < mateBlocks.length; _i2 += 1) {
-                  (_mateChunks = mateChunks).push.apply(_mateChunks, (0, _toConsumableArray2.default)(mateBlocks[_i2]));
-                } // filter out duplicates
-
-
-                mateChunks = (0, _filter.default)(_context6 = (0, _sort.default)(mateChunks).call(mateChunks, function (a, b) {
-                  return a.toString().localeCompare(b.toString());
-                })).call(_context6, function (item, pos, ary) {
-                  return !pos || item.toString() !== ary[pos - 1].toString();
-                });
-                mateRecordPromises = [];
-                mateFeatPromises = [];
-                mateTotalSize = (0, _reduce.default)(_context7 = (0, _map.default)(mateChunks).call(mateChunks, function (s) {
-                  return s.sliceBytes;
-                })).call(_context7, function (a, b) {
-                  return a + b;
-                }, 0);
-
-                if (!(mateTotalSize > this.fetchSizeLimit)) {
-                  _context9.next = 37;
-                  break;
-                }
-
-                throw new Error((0, _concat.default)(_context8 = "mate data size of ".concat(mateTotalSize.toLocaleString(), " bytes exceeded fetch size limit of ")).call(_context8, this.fetchSizeLimit.toLocaleString(), " bytes"));
-
-              case 37:
-                (0, _forEach.default)(mateChunks).call(mateChunks, function (c) {
-                  var recordPromise = _this.cram.featureCache.get(c.toString());
-
-                  if (!recordPromise) {
-                    recordPromise = _this.getRecordsInSlice(c, function () {
-                      return true;
-                    });
-
-                    _this.cram.featureCache.set(c.toString(), recordPromise);
-                  }
-
-                  mateRecordPromises.push(recordPromise);
-                  var featPromise = recordPromise.then(function (feats) {
-                    var mateRecs = [];
-
-                    for (var _i3 = 0; _i3 < feats.length; _i3 += 1) {
-                      var feature = feats[_i3];
-
-                      if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
-                        mateRecs.push(feature);
-                      }
-                    }
-
-                    return mateRecs;
-                  });
-                  mateFeatPromises.push(featPromise);
-                });
-                _context9.next = 40;
-                return _promise.default.all(mateFeatPromises);
-
-              case 40:
-                newMateFeats = _context9.sent;
-
-                if (newMateFeats.length) {
-                  newMates = (0, _reduce.default)(newMateFeats).call(newMateFeats, function (result, current) {
-                    return (0, _concat.default)(result).call(result, current);
-                  });
-                  ret = (0, _concat.default)(ret).call(ret, newMates);
-                }
-
-              case 42:
-                return _context9.abrupt("return", ret);
-
-              case 43:
-              case "end":
-                return _context9.stop();
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
             }
-          }
-        }, _callee, this);
-      }));
-
-      function getRecordsForRange(_x, _x2, _x3) {
-        return _getRecordsForRange.apply(this, arguments);
-      }
-
-      return getRecordsForRange;
-    }()
-  }, {
-    key: "getRecordsInSlice",
-    value: function getRecordsInSlice(_ref3, filterFunction) {
-      var containerStart = _ref3.containerStart,
-          sliceStart = _ref3.sliceStart,
-          sliceBytes = _ref3.sliceBytes;
-      var container = this.cram.getContainerAtPosition(containerStart);
-      var slice = container.getSlice(sliceStart, sliceBytes);
-      return slice.getRecords(filterFunction);
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
     }
+};
+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 cramFile_1 = __importDefault(require("./cramFile"));
+var IndexedCramFile = /** @class */ (function () {
     /**
      *
+     * @param {object} args
+     * @param {CramFile} args.cram
+     * @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
+     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
+     * @param {number} [args.fetchSizeLimit] optional maximum number of bytes to fetch in a single getRecordsForRange call.  Default 3 MiB.
+     * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
+     * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
+     */
+    function IndexedCramFile(args) {
+        // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
+        if (args.cram) {
+            this.cram = args.cram;
+        }
+        else {
+            this.cram = new cramFile_1.default({
+                url: args.cramUrl,
+                path: args.cramPath,
+                filehandle: args.cramFilehandle,
+                seqFetch: args.seqFetch,
+                checkSequenceMD5: args.checkSequenceMD5,
+                cacheSize: args.cacheSize,
+            });
+        }
+        if (!(this.cram instanceof cramFile_1.default)) {
+            throw new Error('invalid arguments: no cramfile');
+        }
+        this.index = args.index;
+        if (!this.index.getEntriesForRange) {
+            throw new Error('invalid arguments: not an index');
+        }
+        this.fetchSizeLimit = args.fetchSizeLimit || 3000000;
+    }
+    /**
+     *
+     * @param {number} seq numeric ID of the reference sequence
+     * @param {number} start start of the range of interest. 1-based closed coordinates.
+     * @param {number} end end of the range of interest. 1-based closed coordinates.
+     * @returns {Promise[Array[CramRecord]]}
+     */
+    IndexedCramFile.prototype.getRecordsForRange = function (seq, start, end, opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var seqId, slices, totalSize, filter, sliceResults, ret, readNames, readIds_1, i, name_1, id, unmatedPairs_1, matePromises, i, name_2, mateSlices, mateBlocks, mateChunks, i, mateRecordPromises_1, mateFeatPromises_1, mateTotalSize, newMateFeats, newMates;
+            var _a;
+            var _this = this;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        opts.viewAsPairs = opts.viewAsPairs || false;
+                        opts.pairAcrossChr = opts.pairAcrossChr || false;
+                        opts.maxInsertSize = opts.maxInsertSize || 200000;
+                        if (typeof seq === 'string') {
+                            // TODO: support string reference sequence names somehow
+                            throw new errors_1.CramUnimplementedError('string sequence names not yet supported');
+                        }
+                        seqId = seq;
+                        return [4 /*yield*/, this.index.getEntriesForRange(seqId, start, end)];
+                    case 1:
+                        slices = _b.sent();
+                        totalSize = slices.map(function (s) { return s.sliceBytes; }).reduce(function (a, b) { return a + b; }, 0);
+                        if (totalSize > this.fetchSizeLimit) {
+                            throw new errors_1.CramSizeLimitError("data size of ".concat(totalSize.toLocaleString(), " bytes exceeded fetch size limit of ").concat(this.fetchSizeLimit.toLocaleString(), " bytes"));
+                        }
+                        filter = function (feature) {
+                            return feature.sequenceId === seq &&
+                                feature.alignmentStart <= end &&
+                                feature.alignmentStart + feature.lengthOnRef - 1 >= start;
+                        };
+                        return [4 /*yield*/, Promise.all(slices.map(function (slice) { return _this.getRecordsInSlice(slice, filter); }))];
+                    case 2:
+                        sliceResults = _b.sent();
+                        ret = (_a = Array.prototype).concat.apply(_a, sliceResults);
+                        if (!opts.viewAsPairs) return [3 /*break*/, 5];
+                        readNames = {};
+                        readIds_1 = {};
+                        for (i = 0; i < ret.length; i += 1) {
+                            name_1 = ret[i].readName;
+                            id = ret[i].uniqueId;
+                            if (!readNames[name_1]) {
+                                readNames[name_1] = 0;
+                            }
+                            readNames[name_1] += 1;
+                            readIds_1[id] = 1;
+                        }
+                        unmatedPairs_1 = {};
+                        Object.entries(readNames).forEach(function (_a) {
+                            var k = _a[0], v = _a[1];
+                            if (v === 1) {
+                                unmatedPairs_1[k] = true;
+                            }
+                        });
+                        matePromises = [];
+                        for (i = 0; i < ret.length; i += 1) {
+                            name_2 = ret[i].readName;
+                            if (unmatedPairs_1[name_2] &&
+                                ret[i].mate &&
+                                (ret[i].mate.sequenceId === seqId || opts.pairAcrossChr) &&
+                                Math.abs(ret[i].alignmentStart - ret[i].mate.alignmentStart) <
+                                    opts.maxInsertSize) {
+                                mateSlices = this.index.getEntriesForRange(ret[i].mate.sequenceId, ret[i].mate.alignmentStart, ret[i].mate.alignmentStart + 1);
+                                matePromises.push(mateSlices);
+                            }
+                        }
+                        return [4 /*yield*/, Promise.all(matePromises)];
+                    case 3:
+                        mateBlocks = _b.sent();
+                        mateChunks = [];
+                        for (i = 0; i < mateBlocks.length; i += 1) {
+                            mateChunks.push.apply(mateChunks, mateBlocks[i]);
+                        }
+                        // filter out duplicates
+                        mateChunks = mateChunks
+                            .sort(function (a, b) { return a.toString().localeCompare(b.toString()); })
+                            .filter(function (item, pos, ary) {
+                            return !pos || item.toString() !== ary[pos - 1].toString();
+                        });
+                        mateRecordPromises_1 = [];
+                        mateFeatPromises_1 = [];
+                        mateTotalSize = mateChunks
+                            .map(function (s) { return s.sliceBytes; })
+                            .reduce(function (a, b) { return a + b; }, 0);
+                        if (mateTotalSize > this.fetchSizeLimit) {
+                            throw new Error("mate data size of ".concat(mateTotalSize.toLocaleString(), " bytes exceeded fetch size limit of ").concat(this.fetchSizeLimit.toLocaleString(), " bytes"));
+                        }
+                        mateChunks.forEach(function (c) {
+                            var recordPromise = _this.cram.featureCache.get(c.toString());
+                            if (!recordPromise) {
+                                recordPromise = _this.getRecordsInSlice(c, function () { return true; });
+                                _this.cram.featureCache.set(c.toString(), recordPromise);
+                            }
+                            mateRecordPromises_1.push(recordPromise);
+                            var featPromise = recordPromise.then(function (feats) {
+                                var mateRecs = [];
+                                for (var i = 0; i < feats.length; i += 1) {
+                                    var feature = feats[i];
+                                    if (unmatedPairs_1[feature.readName] && !readIds_1[feature.uniqueId]) {
+                                        mateRecs.push(feature);
+                                    }
+                                }
+                                return mateRecs;
+                            });
+                            mateFeatPromises_1.push(featPromise);
+                        });
+                        return [4 /*yield*/, Promise.all(mateFeatPromises_1)];
+                    case 4:
+                        newMateFeats = _b.sent();
+                        if (newMateFeats.length) {
+                            newMates = newMateFeats.reduce(function (result, current) {
+                                return result.concat(current);
+                            });
+                            ret = ret.concat(newMates);
+                        }
+                        _b.label = 5;
+                    case 5: return [2 /*return*/, ret];
+                }
+            });
+        });
+    };
+    IndexedCramFile.prototype.getRecordsInSlice = function (_a, filterFunction) {
+        var containerStart = _a.containerStart, sliceStart = _a.sliceStart, sliceBytes = _a.sliceBytes;
+        var container = this.cram.getContainerAtPosition(containerStart);
+        var slice = container.getSlice(sliceStart, sliceBytes);
+        return slice.getRecords(filterFunction);
+    };
+    /**
+     *
      * @param {number} seqId
@@ -315,12 +217,8 @@ * @returns {Promise} true if the CRAM file contains data for the given
      */
-
-  }, {
-    key: "hasDataForReferenceSequence",
-    value: function hasDataForReferenceSequence(seqId) {
-      return this.index.hasDataForReferenceSequence(seqId);
-    }
-  }]);
-  return IndexedCramFile;
-}();
-
-module.exports = IndexedCramFile;
+    IndexedCramFile.prototype.hasDataForReferenceSequence = function (seqId) {
+        return this.index.hasDataForReferenceSequence(seqId);
+    };
+    return IndexedCramFile;
+}());
+exports.default = IndexedCramFile;
+//# sourceMappingURL=indexedCramFile.js.map

dist/io/bufferCache.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _promise = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/promise"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var LRU = require('quick-lru');
-
-var BufferCache =
-/*#__PURE__*/
-function () {
-  function BufferCache(_ref) {
-    var fetch = _ref.fetch,
-        _ref$size = _ref.size,
-        size = _ref$size === void 0 ? 10000000 : _ref$size,
-        _ref$chunkSize = _ref.chunkSize,
-        chunkSize = _ref$chunkSize === void 0 ? 32768 : _ref$chunkSize;
-    (0, _classCallCheck2.default)(this, BufferCache);
-    if (!fetch) throw new Error('fetch function required');
-    this.fetch = fetch;
-    this.chunkSize = chunkSize;
-    this.lruCache = new LRU({
-      maxSize: Math.floor(size / chunkSize)
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
-  }
-
-  (0, _createClass2.default)(BufferCache, [{
-    key: "get",
-    value: function () {
-      var _get = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee(outputBuffer, offset, length, position) {
-        var _this = this;
-
-        var firstChunk, lastChunk, fetches, _loop, chunk, chunks, chunksOffset;
-
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                if (!(outputBuffer.length < offset + length)) {
-                  _context.next = 2;
-                  break;
-                }
-
-                throw new Error('output buffer not big enough for request');
-
-              case 2:
-                // calculate the list of chunks involved in this fetch
-                firstChunk = Math.floor(position / this.chunkSize);
-                lastChunk = Math.floor((position + length) / this.chunkSize); // fetch them all as necessary
-
-                fetches = new Array(lastChunk - firstChunk + 1);
-
-                _loop = function _loop(chunk) {
-                  fetches[chunk - firstChunk] = _this._getChunk(chunk).then(function (data) {
-                    return {
-                      data: data,
-                      chunkNumber: chunk
-                    };
-                  });
-                };
-
-                for (chunk = firstChunk; chunk <= lastChunk; chunk += 1) {
-                  _loop(chunk);
-                } // stitch together the response buffer using them
-
-
-                _context.next = 9;
-                return _promise.default.all(fetches);
-
-              case 9:
-                chunks = _context.sent;
-                chunksOffset = position - chunks[0].chunkNumber * this.chunkSize;
-                (0, _forEach.default)(chunks).call(chunks, function (_ref2) {
-                  var data = _ref2.data,
-                      chunkNumber = _ref2.chunkNumber;
-                  var chunkPositionStart = chunkNumber * _this.chunkSize;
-                  var copyStart = 0;
-                  var copyEnd = _this.chunkSize;
-                  var copyOffset = offset + (chunkNumber - firstChunk) * _this.chunkSize - chunksOffset;
-
-                  if (chunkNumber === firstChunk) {
-                    copyOffset = offset;
-                    copyStart = chunksOffset;
-                  }
-
-                  if (chunkNumber === lastChunk) {
-                    copyEnd = position + length - chunkPositionStart;
-                  }
-
-                  data.copy(outputBuffer, copyOffset, copyStart, copyEnd);
-                });
-
-              case 12:
-              case "end":
-                return _context.stop();
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
             }
-          }
-        }, _callee, this);
-      }));
-
-      function get(_x, _x2, _x3, _x4) {
-        return _get.apply(this, arguments);
-      }
-
-      return get;
-    }()
-  }, {
-    key: "_getChunk",
-    value: function _getChunk(chunkNumber) {
-      var cachedPromise = this.lruCache.get(chunkNumber);
-      if (cachedPromise) return cachedPromise;
-      var freshPromise = this.fetch(chunkNumber * this.chunkSize, this.chunkSize);
-      this.lruCache.set(chunkNumber, freshPromise);
-      return freshPromise;
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
     }
-  }]);
-  return BufferCache;
-}();
-
-module.exports = BufferCache;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var quick_lru_1 = __importDefault(require("quick-lru"));
+var BufferCache = /** @class */ (function () {
+    function BufferCache(_a) {
+        var fetch = _a.fetch, _b = _a.size, size = _b === void 0 ? 10000000 : _b, _c = _a.chunkSize, chunkSize = _c === void 0 ? 32768 : _c;
+        if (!fetch) {
+            throw new Error('fetch function required');
+        }
+        this.fetch = fetch;
+        this.chunkSize = chunkSize;
+        this.lruCache = new quick_lru_1.default({ maxSize: Math.floor(size / chunkSize) });
+    }
+    BufferCache.prototype.get = function (outputBuffer, offset, length, position) {
+        return __awaiter(this, void 0, void 0, function () {
+            var firstChunk, lastChunk, fetches, _loop_1, this_1, chunk, chunks, chunksOffset;
+            var _this = this;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        if (outputBuffer.length < offset + length) {
+                            throw new Error('output buffer not big enough for request');
+                        }
+                        firstChunk = Math.floor(position / this.chunkSize);
+                        lastChunk = Math.floor((position + length) / this.chunkSize);
+                        fetches = new Array(lastChunk - firstChunk + 1);
+                        _loop_1 = function (chunk) {
+                            fetches[chunk - firstChunk] = this_1._getChunk(chunk).then(function (data) { return ({
+                                data: data,
+                                chunkNumber: chunk,
+                            }); });
+                        };
+                        this_1 = this;
+                        for (chunk = firstChunk; chunk <= lastChunk; chunk += 1) {
+                            _loop_1(chunk);
+                        }
+                        return [4 /*yield*/, Promise.all(fetches)];
+                    case 1:
+                        chunks = _a.sent();
+                        chunksOffset = position - chunks[0].chunkNumber * this.chunkSize;
+                        chunks.forEach(function (_a) {
+                            var data = _a.data, chunkNumber = _a.chunkNumber;
+                            var chunkPositionStart = chunkNumber * _this.chunkSize;
+                            var copyStart = 0;
+                            var copyEnd = _this.chunkSize;
+                            var copyOffset = offset + (chunkNumber - firstChunk) * _this.chunkSize - chunksOffset;
+                            if (chunkNumber === firstChunk) {
+                                copyOffset = offset;
+                                copyStart = chunksOffset;
+                            }
+                            if (chunkNumber === lastChunk) {
+                                copyEnd = position + length - chunkPositionStart;
+                            }
+                            data.copy(outputBuffer, copyOffset, copyStart, copyEnd);
+                        });
+                        return [2 /*return*/];
+                }
+            });
+        });
+    };
+    BufferCache.prototype._getChunk = function (chunkNumber) {
+        var cachedPromise = this.lruCache.get(chunkNumber);
+        if (cachedPromise) {
+            return cachedPromise;
+        }
+        var freshPromise = this.fetch(chunkNumber * this.chunkSize, this.chunkSize);
+        this.lruCache.set(chunkNumber, freshPromise);
+        return freshPromise;
+    };
+    return BufferCache;
+}());
+exports.default = BufferCache;
+//# sourceMappingURL=bufferCache.js.map

dist/io/index.js

 "use strict";
-
-var url = require('url');
-
-var RemoteFile = require('./remoteFile');
-
-var LocalFile = require('./localFile');
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.open = exports.fromUrl = exports.RemoteFile = exports.LocalFile = void 0;
+var url_1 = __importDefault(require("url"));
+var remoteFile_1 = __importDefault(require("./remoteFile"));
+exports.RemoteFile = remoteFile_1.default;
+var localFile_1 = __importDefault(require("./localFile"));
+exports.LocalFile = localFile_1.default;
 function fromUrl(source) {
-  var _url$parse = url.parse(source),
-      protocol = _url$parse.protocol,
-      pathname = _url$parse.pathname;
-
-  if (protocol === 'file:') {
-    return new LocalFile(unescape(pathname));
-  }
-
-  return new RemoteFile(source);
+    var _a = url_1.default.parse(source), protocol = _a.protocol, pathname = _a.pathname;
+    if (protocol === 'file:') {
+        return new localFile_1.default(unescape(pathname));
+    }
+    return new remoteFile_1.default(source);
 }
-
-module.exports = {
-  LocalFile: LocalFile,
-  RemoteFile: RemoteFile,
-  fromUrl: fromUrl,
-  open: function open(maybeUrl, maybePath, maybeFilehandle) {
-    if (maybeFilehandle) return maybeFilehandle;
-    if (maybeUrl) return fromUrl(maybeUrl);
-    if (maybePath) return new LocalFile(maybePath);
+exports.fromUrl = fromUrl;
+function open(maybeUrl, maybePath, maybeFilehandle) {
+    if (maybeFilehandle) {
+        return maybeFilehandle;
+    }
+    if (maybeUrl) {
+        return fromUrl(maybeUrl);
+    }
+    if (maybePath) {
+        return new localFile_1.default(maybePath);
+    }
     throw new Error('no url, path, or filehandle provided, cannot open');
-  }
-};
+}
+exports.open = open;
+//# sourceMappingURL=index.js.map

dist/io/localFile.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _require = require('es6-promisify'),
-    promisify = _require.promisify; // don't load fs native module if running in webpacked code
-
-
-var fs = typeof __webpack_require__ !== 'function' ? require('fs') : null; // eslint-disable-line camelcase
-
-var fsOpen = fs && promisify(fs.open);
-var fsRead = fs && promisify(fs.read);
-var fsFStat = fs && promisify(fs.fstat);
-var fsReadFile = fs && promisify(fs.readFile);
-
-var LocalFile =
-/*#__PURE__*/
-function () {
-  function LocalFile(source) {
-    (0, _classCallCheck2.default)(this, LocalFile);
-    this.position = 0;
-    this.filename = source;
-    this.fd = fsOpen(this.filename, 'r');
-  }
-
-  (0, _createClass2.default)(LocalFile, [{
-    key: "read",
-    value: function () {
-      var _read = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee(buffer) {
-        var offset,
-            length,
-            position,
-            readPosition,
-            _args = arguments;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                offset = _args.length > 1 && _args[1] !== undefined ? _args[1] : 0;
-                length = _args.length > 2 ? _args[2] : undefined;
-                position = _args.length > 3 ? _args[3] : undefined;
-                readPosition = position;
-
-                if (readPosition === null) {
-                  readPosition = this.position;
-                  this.position += length;
-                }
-
-                _context.t0 = fsRead;
-                _context.next = 8;
-                return this.fd;
-
-              case 8:
-                _context.t1 = _context.sent;
-                _context.t2 = buffer;
-                _context.t3 = offset;
-                _context.t4 = length;
-                _context.t5 = position;
-                return _context.abrupt("return", (0, _context.t0)(_context.t1, _context.t2, _context.t3, _context.t4, _context.t5));
-
-              case 14:
-              case "end":
-                return _context.stop();
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
             }
-          }
-        }, _callee, this);
-      }));
-
-      function read(_x) {
-        return _read.apply(this, arguments);
-      }
-
-      return read;
-    }()
-  }, {
-    key: "readFile",
-    value: function () {
-      var _readFile = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee2() {
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.t0 = fsReadFile;
-                _context2.next = 3;
-                return this.fd;
-
-              case 3:
-                _context2.t1 = _context2.sent;
-                return _context2.abrupt("return", (0, _context2.t0)(_context2.t1));
-
-              case 5:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function readFile() {
-        return _readFile.apply(this, arguments);
-      }
-
-      return readFile;
-    }()
-  }, {
-    key: "stat",
-    value: function () {
-      var _stat = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee3() {
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                if (this._stat) {
-                  _context3.next = 8;
-                  break;
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var es6_promisify_1 = require("es6-promisify");
+var fs_1 = __importDefault(require("fs"));
+var fsOpen = fs_1.default && (0, es6_promisify_1.promisify)(fs_1.default.open);
+var fsRead = fs_1.default && (0, es6_promisify_1.promisify)(fs_1.default.read);
+var fsFStat = fs_1.default && (0, es6_promisify_1.promisify)(fs_1.default.fstat);
+var fsReadFile = fs_1.default && (0, es6_promisify_1.promisify)(fs_1.default.readFile);
+var LocalFile = /** @class */ (function () {
+    function LocalFile(source) {
+        this.position = 0;
+        this.filename = source;
+        this.fd = fsOpen(this.filename, 'r');
+    }
+    LocalFile.prototype.read = function (buffer, offset, length, position) {
+        if (offset === void 0) { offset = 0; }
+        return __awaiter(this, void 0, void 0, function () {
+            var readPosition, _a;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        readPosition = position;
+                        if (readPosition === null) {
+                            readPosition = this.position;
+                            this.position += length;
+                        }
+                        _a = fsRead;
+                        return [4 /*yield*/, this.fd];
+                    case 1: return [2 /*return*/, _a.apply(void 0, [_b.sent(), buffer, offset, length, position])];
                 }
-
-                _context3.t0 = fsFStat;
-                _context3.next = 4;
-                return this.fd;
-
-              case 4:
-                _context3.t1 = _context3.sent;
-                _context3.next = 7;
-                return (0, _context3.t0)(_context3.t1);
-
-              case 7:
-                this._stat = _context3.sent;
-
-              case 8:
-                return _context3.abrupt("return", this._stat);
-
-              case 9:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function stat() {
-        return _stat.apply(this, arguments);
-      }
-
-      return stat;
-    }()
-  }]);
-  return LocalFile;
-}();
-
-module.exports = LocalFile;
+            });
+        });
+    };
+    LocalFile.prototype.readFile = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var _a;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        _a = fsReadFile;
+                        return [4 /*yield*/, this.fd];
+                    case 1: return [2 /*return*/, _a.apply(void 0, [_b.sent()])];
+                }
+            });
+        });
+    };
+    LocalFile.prototype.stat = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var _a, _b;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0:
+                        if (!!this._stat) return [3 /*break*/, 3];
+                        _a = this;
+                        _b = fsFStat;
+                        return [4 /*yield*/, this.fd];
+                    case 1: return [4 /*yield*/, _b.apply(void 0, [_c.sent()])];
+                    case 2:
+                        _a._stat = _c.sent();
+                        _c.label = 3;
+                    case 3: return [2 /*return*/, this._stat];
+                }
+            });
+        });
+    };
+    return LocalFile;
+}());
+exports.default = LocalFile;
+//# sourceMappingURL=localFile.js.map

dist/io/remoteFile.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime-corejs3/regenerator"));
-
-var _parseInt2 = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/parse-int"));
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/asyncToGenerator"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var fetch = require('cross-fetch');
-
-var BufferCache = require('./bufferCache');
-
-var RemoteFile =
-/*#__PURE__*/
-function () {
-  function RemoteFile(source) {
-    var _this = this;
-
-    (0, _classCallCheck2.default)(this, RemoteFile);
-    this.position = 0;
-    this.url = source;
-    this.cache = new BufferCache({
-      fetch: function fetch(start, length) {
-        return _this._fetch(start, length);
-      }
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
-  }
-
-  (0, _createClass2.default)(RemoteFile, [{
-    key: "_fetch",
-    value: function () {
-      var _fetch2 = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee(position, length) {
-        var _context2;
-
-        var headers, _context, response, nodeBuffer, sizeMatch;
-
-        return _regenerator.default.wrap(function _callee$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                headers = {};
-
-                if (length < Infinity) {
-                  headers.range = (0, _concat.default)(_context = "bytes=".concat(position, "-")).call(_context, position + length);
-                } else if (length === Infinity && position !== 0) {
-                  headers.range = "bytes=".concat(position, "-");
-                }
-
-                _context3.next = 4;
-                return fetch(this.url, {
-                  method: 'GET',
-                  headers: headers,
-                  redirect: 'follow',
-                  mode: 'cors'
-                });
-
-              case 4:
-                response = _context3.sent;
-
-                if (!(response.status === 200 && position === 0 || response.status === 206)) {
-                  _context3.next = 14;
-                  break;
-                }
-
-                _context3.t0 = Buffer;
-                _context3.next = 9;
-                return response.arrayBuffer();
-
-              case 9:
-                _context3.t1 = _context3.sent;
-                nodeBuffer = _context3.t0.from.call(_context3.t0, _context3.t1);
-                // try to parse out the size of the remote file
-                sizeMatch = /\/(\d+)$/.exec(response.headers.get('content-range'));
-                if (sizeMatch[1]) this._stat = {
-                  size: (0, _parseInt2.default)(sizeMatch[1], 10)
-                };
-                return _context3.abrupt("return", nodeBuffer);
-
-              case 14:
-                throw new Error((0, _concat.default)(_context2 = "HTTP ".concat(response.status, " fetching ")).call(_context2, this.url));
-
-              case 15:
-              case "end":
-                return _context3.stop();
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
             }
-          }
-        }, _callee, this);
-      }));
-
-      function _fetch(_x, _x2) {
-        return _fetch2.apply(this, arguments);
-      }
-
-      return _fetch;
-    }()
-  }, {
-    key: "read",
-    value: function read(buffer) {
-      var offset = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0;
-      var length = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : Infinity;
-      var position = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : 0;
-      var readPosition = position;
-
-      if (readPosition === null) {
-        readPosition = this.position;
-        this.position += length;
-      }
-
-      return this.cache.get(buffer, offset, length, position);
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
     }
-  }, {
-    key: "readFile",
-    value: function () {
-      var _readFile = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee2() {
-        var response;
-        return _regenerator.default.wrap(function _callee2$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return fetch(this.url, {
-                  method: 'GET',
-                  redirect: 'follow',
-                  mode: 'cors'
-                });
-
-              case 2:
-                response = _context4.sent;
-                _context4.t0 = Buffer;
-                _context4.next = 6;
-                return response.arrayBuffer();
-
-              case 6:
-                _context4.t1 = _context4.sent;
-                return _context4.abrupt("return", _context4.t0.from.call(_context4.t0, _context4.t1));
-
-              case 8:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function readFile() {
-        return _readFile.apply(this, arguments);
-      }
-
-      return readFile;
-    }()
-  }, {
-    key: "stat",
-    value: function () {
-      var _stat = (0, _asyncToGenerator2.default)(
-      /*#__PURE__*/
-      _regenerator.default.mark(function _callee3() {
-        var buf;
-        return _regenerator.default.wrap(function _callee3$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
-                if (this._stat) {
-                  _context5.next = 6;
-                  break;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var cross_fetch_1 = __importDefault(require("cross-fetch"));
+var bufferCache_1 = __importDefault(require("./bufferCache"));
+var RemoteFile = /** @class */ (function () {
+    function RemoteFile(source) {
+        var _this = this;
+        this.position = 0;
+        this.url = source;
+        this.cache = new bufferCache_1.default({
+            fetch: function (start, length) { return _this._fetch(start, length); },
+        });
+    }
+    RemoteFile.prototype._fetch = function (position, length) {
+        return __awaiter(this, void 0, void 0, function () {
+            var headers, response, nodeBuffer, _a, _b, sizeMatch;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0:
+                        headers = {};
+                        if (length < Infinity) {
+                            headers.range = "bytes=".concat(position, "-").concat(position + length);
+                        }
+                        else if (length === Infinity && position !== 0) {
+                            headers.range = "bytes=".concat(position, "-");
+                        }
+                        return [4 /*yield*/, (0, cross_fetch_1.default)(this.url, {
+                                method: 'GET',
+                                headers: headers,
+                                redirect: 'follow',
+                                mode: 'cors',
+                            })];
+                    case 1:
+                        response = _c.sent();
+                        if (!((response.status === 200 && position === 0) ||
+                            response.status === 206)) return [3 /*break*/, 3];
+                        _b = (_a = Buffer).from;
+                        return [4 /*yield*/, response.arrayBuffer()];
+                    case 2:
+                        nodeBuffer = _b.apply(_a, [_c.sent()]);
+                        sizeMatch = /\/(\d+)$/.exec(response.headers.get('content-range'));
+                        if (sizeMatch[1]) {
+                            this._stat = { size: parseInt(sizeMatch[1], 10) };
+                        }
+                        return [2 /*return*/, nodeBuffer];
+                    case 3: throw new Error("HTTP ".concat(response.status, " fetching ").concat(this.url));
                 }
-
-                buf = Buffer.allocUnsafe(10);
-                _context5.next = 4;
-                return this.read(buf, 0, 10, 0);
-
-              case 4:
-                if (this._stat) {
-                  _context5.next = 6;
-                  break;
+            });
+        });
+    };
+    RemoteFile.prototype.read = function (buffer, offset, length, position) {
+        if (offset === void 0) { offset = 0; }
+        if (length === void 0) { length = Infinity; }
+        if (position === void 0) { position = 0; }
+        var readPosition = position;
+        if (readPosition === null) {
+            readPosition = this.position;
+            this.position += length;
+        }
+        return this.cache.get(buffer, offset, length, position);
+    };
+    RemoteFile.prototype.readFile = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var response, _a, _b;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0: return [4 /*yield*/, (0, cross_fetch_1.default)(this.url, {
+                            method: 'GET',
+                            redirect: 'follow',
+                            mode: 'cors',
+                        })];
+                    case 1:
+                        response = _c.sent();
+                        _b = (_a = Buffer).from;
+                        return [4 /*yield*/, response.arrayBuffer()];
+                    case 2: return [2 /*return*/, _b.apply(_a, [_c.sent()])];
                 }
-
-                throw new Error("unable to determine size of file at ".concat(this.url));
-
-              case 6:
-                return _context5.abrupt("return", this._stat);
-
-              case 7:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function stat() {
-        return _stat.apply(this, arguments);
-      }
-
-      return stat;
-    }()
-  }]);
-  return RemoteFile;
-}();
-
-module.exports = RemoteFile;
+            });
+        });
+    };
+    RemoteFile.prototype.stat = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var buf;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        if (!!this._stat) return [3 /*break*/, 2];
+                        buf = Buffer.allocUnsafe(10);
+                        return [4 /*yield*/, this.read(buf, 0, 10, 0)];
+                    case 1:
+                        _a.sent();
+                        if (!this._stat) {
+                            throw new Error("unable to determine size of file at ".concat(this.url));
+                        }
+                        _a.label = 2;
+                    case 2: return [2 /*return*/, this._stat];
+                }
+            });
+        });
+    };
+    return RemoteFile;
+}());
+exports.default = RemoteFile;
+//# sourceMappingURL=remoteFile.js.map

dist/rans/constants.js

 "use strict";
-
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RANS_BYTE_L = exports.TOTFREQ = exports.TF_SHIFT = void 0;
 var TF_SHIFT = 12;
+exports.TF_SHIFT = TF_SHIFT;
 var TOTFREQ = 1 << TF_SHIFT;
+exports.TOTFREQ = TOTFREQ;
 var RANS_BYTE_L = 1 << 23;
-module.exports = {
-  TF_SHIFT: TF_SHIFT,
-  TOTFREQ: TOTFREQ,
-  RANS_BYTE_L: RANS_BYTE_L
-};
+exports.RANS_BYTE_L = RANS_BYTE_L;
+//# sourceMappingURL=constants.js.map

dist/rans/d04.js

 "use strict";
-
-var _require = require('../errors'),
-    CramMalformedError = _require.CramMalformedError;
-
-var Constants = require('./constants');
-
-var Decoding = require('./decoding');
-
+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 constants_1 = require("./constants");
+var decoding_1 = __importDefault(require("./decoding"));
 function uncompress(
-/* ByteBuffer */
-input,
-/* Decoding.AriDecoder */
-D,
-/* Decoding.Symbol[] */
-syms,
-/* ByteBuffer */
-out) {
-  var rans0 = input.getInt();
-  var rans1 = input.getInt();
-  var rans2 = input.getInt();
-  var rans3 = input.getInt();
-  var
-  /* int */
-  outputSize = out.remaining();
-  var
-  /* int */
-  outputEnd = outputSize & ~3;
-
-  for (var i = 0; i < outputEnd; i += 4) {
-    var
-    /* byte */
-    c0 = D.R[Decoding.get(rans0, Constants.TF_SHIFT)];
-    var
-    /* byte */
-    c1 = D.R[Decoding.get(rans1, Constants.TF_SHIFT)];
-    var
-    /* byte */
-    c2 = D.R[Decoding.get(rans2, Constants.TF_SHIFT)];
-    var
-    /* byte */
-    c3 = D.R[Decoding.get(rans3, Constants.TF_SHIFT)];
-    out.putAt(i, c0);
-    out.putAt(i + 1, c1);
-    out.putAt(i + 2, c2);
-    out.putAt(i + 3, c3);
-    rans0 = Decoding.advanceSymbolStep(rans0, syms[0xff & c0], Constants.TF_SHIFT);
-    rans1 = Decoding.advanceSymbolStep(rans1, syms[0xff & c1], Constants.TF_SHIFT);
-    rans2 = Decoding.advanceSymbolStep(rans2, syms[0xff & c2], Constants.TF_SHIFT);
-    rans3 = Decoding.advanceSymbolStep(rans3, syms[0xff & c3], Constants.TF_SHIFT);
-    rans0 = Decoding.renormalize(rans0, input);
-    rans1 = Decoding.renormalize(rans1, input);
-    rans2 = Decoding.renormalize(rans2, input);
-    rans3 = Decoding.renormalize(rans3, input);
-  }
-
-  out.setPosition(outputEnd);
-  var
-  /* byte */
-  c;
-
-  switch (outputSize & 3) {
-    case 0:
-      break;
-
-    case 1:
-      c = D.R[Decoding.get(rans0, Constants.TF_SHIFT)];
-      Decoding.advanceSymbol(rans0, input, syms[0xff & c], Constants.TF_SHIFT);
-      out.put(c);
-      break;
-
-    case 2:
-      c = D.R[Decoding.get(rans0, Constants.TF_SHIFT)];
-      Decoding.advanceSymbol(rans0, input, syms[0xff & c], Constants.TF_SHIFT);
-      out.put(c);
-      c = D.R[Decoding.get(rans1, Constants.TF_SHIFT)];
-      Decoding.advanceSymbol(rans1, input, syms[0xff & c], Constants.TF_SHIFT);
-      out.put(c);
-      break;
-
-    case 3:
-      c = D.R[Decoding.get(rans0, Constants.TF_SHIFT)];
-      Decoding.advanceSymbol(rans0, input, syms[0xff & c], Constants.TF_SHIFT);
-      out.put(c);
-      c = D.R[Decoding.get(rans1, Constants.TF_SHIFT)];
-      Decoding.advanceSymbol(rans1, input, syms[0xff & c], Constants.TF_SHIFT);
-      out.put(c);
-      c = D.R[Decoding.get(rans2, Constants.TF_SHIFT)];
-      Decoding.advanceSymbol(rans2, input, syms[0xff & c], Constants.TF_SHIFT);
-      out.put(c);
-      break;
-
-    default:
-      throw new CramMalformedError('invalid output size encountered during rANS decoding');
-  }
-
-  out.setPosition(0);
+/* ByteBuffer */ input, 
+/* Decoding.AriDecoder */ D, 
+/* Decoding.Symbol[] */ syms, 
+/* ByteBuffer */ out) {
+    var rans0 = input.getInt();
+    var rans1 = input.getInt();
+    var rans2 = input.getInt();
+    var rans3 = input.getInt();
+    var /* int */ outputSize = out.remaining();
+    var /* int */ outputEnd = outputSize & ~3;
+    for (var i = 0; i < outputEnd; i += 4) {
+        var /* byte */ c0 = D.R[decoding_1.default.get(rans0, constants_1.TF_SHIFT)];
+        var /* byte */ c1 = D.R[decoding_1.default.get(rans1, constants_1.TF_SHIFT)];
+        var /* byte */ c2 = D.R[decoding_1.default.get(rans2, constants_1.TF_SHIFT)];
+        var /* byte */ c3 = D.R[decoding_1.default.get(rans3, constants_1.TF_SHIFT)];
+        out.putAt(i, c0);
+        out.putAt(i + 1, c1);
+        out.putAt(i + 2, c2);
+        out.putAt(i + 3, c3);
+        rans0 = decoding_1.default.advanceSymbolStep(rans0, syms[0xff & c0], constants_1.TF_SHIFT);
+        rans1 = decoding_1.default.advanceSymbolStep(rans1, syms[0xff & c1], constants_1.TF_SHIFT);
+        rans2 = decoding_1.default.advanceSymbolStep(rans2, syms[0xff & c2], constants_1.TF_SHIFT);
+        rans3 = decoding_1.default.advanceSymbolStep(rans3, syms[0xff & c3], constants_1.TF_SHIFT);
+        rans0 = decoding_1.default.renormalize(rans0, input);
+        rans1 = decoding_1.default.renormalize(rans1, input);
+        rans2 = decoding_1.default.renormalize(rans2, input);
+        rans3 = decoding_1.default.renormalize(rans3, input);
+    }
+    out.setPosition(outputEnd);
+    var /* byte */ c;
+    switch (outputSize & 3) {
+        case 0:
+            break;
+        case 1:
+            c = D.R[decoding_1.default.get(rans0, constants_1.TF_SHIFT)];
+            decoding_1.default.advanceSymbol(rans0, input, syms[0xff & c], constants_1.TF_SHIFT);
+            out.put(c);
+            break;
+        case 2:
+            c = D.R[decoding_1.default.get(rans0, constants_1.TF_SHIFT)];
+            decoding_1.default.advanceSymbol(rans0, input, syms[0xff & c], constants_1.TF_SHIFT);
+            out.put(c);
+            c = D.R[decoding_1.default.get(rans1, constants_1.TF_SHIFT)];
+            decoding_1.default.advanceSymbol(rans1, input, syms[0xff & c], constants_1.TF_SHIFT);
+            out.put(c);
+            break;
+        case 3:
+            c = D.R[decoding_1.default.get(rans0, constants_1.TF_SHIFT)];
+            decoding_1.default.advanceSymbol(rans0, input, syms[0xff & c], constants_1.TF_SHIFT);
+            out.put(c);
+            c = D.R[decoding_1.default.get(rans1, constants_1.TF_SHIFT)];
+            decoding_1.default.advanceSymbol(rans1, input, syms[0xff & c], constants_1.TF_SHIFT);
+            out.put(c);
+            c = D.R[decoding_1.default.get(rans2, constants_1.TF_SHIFT)];
+            decoding_1.default.advanceSymbol(rans2, input, syms[0xff & c], constants_1.TF_SHIFT);
+            out.put(c);
+            break;
+        default:
+            throw new errors_1.CramMalformedError('invalid output size encountered during rANS decoding');
+    }
+    out.setPosition(0);
 }
-
-module.exports = {
-  uncompress: uncompress
-};
+exports.default = uncompress;
+//# sourceMappingURL=d04.js.map

dist/rans/d14.js

 "use strict";
-
-var Constants = require('./constants');
-
-var Decoding = require('./decoding');
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var constants_1 = require("./constants");
+var decoding_1 = __importDefault(require("./decoding"));
 function uncompress(
-/* ByteBuffer */
-input,
-/* ByteBuffer */
-output,
-/* Decoding.AriDecoder[] */
-D,
-/* Decoding.Symbol[][] */
-syms) {
-  var
-  /* int */
-  outputSize = output.remaining();
-  var rans0 = input.getInt();
-  var rans1 = input.getInt();
-  var rans2 = input.getInt();
-  var rans7 = input.getInt();
-  var
-  /* int */
-  isz4 = outputSize >> 2;
-  var
-  /* int */
-  i0 = 0;
-  var
-  /* int */
-  i1 = isz4;
-  var
-  /* int */
-  i2 = 2 * isz4;
-  var
-  /* int */
-  i7 = 3 * isz4;
-  var
-  /* int */
-  l0 = 0;
-  var
-  /* int */
-  l1 = 0;
-  var
-  /* int */
-  l2 = 0;
-  var
-  /* int */
-  l7 = 0;
-
-  for (; i0 < isz4; i0 += 1, i1 += 1, i2 += 1, i7 += 1) {
-    var
-    /* int */
-    c0 = 0xff & D[l0].R[Decoding.get(rans0, Constants.TF_SHIFT)];
-    var
-    /* int */
-    c1 = 0xff & D[l1].R[Decoding.get(rans1, Constants.TF_SHIFT)];
-    var
-    /* int */
-    c2 = 0xff & D[l2].R[Decoding.get(rans2, Constants.TF_SHIFT)];
-    var
-    /* int */
-    c7 = 0xff & D[l7].R[Decoding.get(rans7, Constants.TF_SHIFT)];
-    output.putAt(i0, c0);
-    output.putAt(i1, c1);
-    output.putAt(i2, c2);
-    output.putAt(i7, c7);
-    rans0 = Decoding.advanceSymbolStep(rans0, syms[l0][c0], Constants.TF_SHIFT);
-    rans1 = Decoding.advanceSymbolStep(rans1, syms[l1][c1], Constants.TF_SHIFT);
-    rans2 = Decoding.advanceSymbolStep(rans2, syms[l2][c2], Constants.TF_SHIFT);
-    rans7 = Decoding.advanceSymbolStep(rans7, syms[l7][c7], Constants.TF_SHIFT);
-    rans0 = Decoding.renormalize(rans0, input);
-    rans1 = Decoding.renormalize(rans1, input);
-    rans2 = Decoding.renormalize(rans2, input);
-    rans7 = Decoding.renormalize(rans7, input);
-    l0 = c0;
-    l1 = c1;
-    l2 = c2;
-    l7 = c7;
-  } // Remainder
-
-
-  for (; i7 < outputSize; i7 += 1) {
-    var
-    /* int */
-    _c = 0xff & D[l7].R[Decoding.get(rans7, Constants.TF_SHIFT)];
-
-    output.putAt(i7, _c);
-    rans7 = Decoding.advanceSymbol(rans7, input, syms[l7][_c], Constants.TF_SHIFT);
-    l7 = _c;
-  }
+/* ByteBuffer */ input, 
+/* ByteBuffer */ output, 
+/* Decoding.AriDecoder[] */ D, 
+/* Decoding.Symbol[][] */ syms) {
+    var /* int */ outputSize = output.remaining();
+    var rans0 = input.getInt();
+    var rans1 = input.getInt();
+    var rans2 = input.getInt();
+    var rans7 = input.getInt();
+    var /* int */ isz4 = outputSize >> 2;
+    var /* int */ i0 = 0;
+    var /* int */ i1 = isz4;
+    var /* int */ i2 = 2 * isz4;
+    var /* int */ i7 = 3 * isz4;
+    var /* int */ l0 = 0;
+    var /* int */ l1 = 0;
+    var /* int */ l2 = 0;
+    var /* int */ l7 = 0;
+    for (; i0 < isz4; i0 += 1, i1 += 1, i2 += 1, i7 += 1) {
+        var /* int */ c0 = 0xff & D[l0].R[decoding_1.default.get(rans0, constants_1.TF_SHIFT)];
+        var /* int */ c1 = 0xff & D[l1].R[decoding_1.default.get(rans1, constants_1.TF_SHIFT)];
+        var /* int */ c2 = 0xff & D[l2].R[decoding_1.default.get(rans2, constants_1.TF_SHIFT)];
+        var /* int */ c7 = 0xff & D[l7].R[decoding_1.default.get(rans7, constants_1.TF_SHIFT)];
+        output.putAt(i0, c0);
+        output.putAt(i1, c1);
+        output.putAt(i2, c2);
+        output.putAt(i7, c7);
+        rans0 = decoding_1.default.advanceSymbolStep(rans0, syms[l0][c0], constants_1.TF_SHIFT);
+        rans1 = decoding_1.default.advanceSymbolStep(rans1, syms[l1][c1], constants_1.TF_SHIFT);
+        rans2 = decoding_1.default.advanceSymbolStep(rans2, syms[l2][c2], constants_1.TF_SHIFT);
+        rans7 = decoding_1.default.advanceSymbolStep(rans7, syms[l7][c7], constants_1.TF_SHIFT);
+        rans0 = decoding_1.default.renormalize(rans0, input);
+        rans1 = decoding_1.default.renormalize(rans1, input);
+        rans2 = decoding_1.default.renormalize(rans2, input);
+        rans7 = decoding_1.default.renormalize(rans7, input);
+        l0 = c0;
+        l1 = c1;
+        l2 = c2;
+        l7 = c7;
+    }
+    // Remainder
+    for (; i7 < outputSize; i7 += 1) {
+        var /* int */ c7 = 0xff & D[l7].R[decoding_1.default.get(rans7, constants_1.TF_SHIFT)];
+        output.putAt(i7, c7);
+        rans7 = decoding_1.default.advanceSymbol(rans7, input, syms[l7][c7], constants_1.TF_SHIFT);
+        l7 = c7;
+    }
 }
-
-module.exports = {
-  uncompress: uncompress
-};
+exports.default = uncompress;
+//# sourceMappingURL=d14.js.map

dist/rans/decoding.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _require = require('../errors'),
-    CramMalformedError = _require.CramMalformedError;
-
-var Constants = require('./constants');
-
-var FC = // int F, C;
-function FC() {
-  (0, _classCallCheck2.default)(this, FC);
-  this.F = undefined;
-  this.C = undefined;
-};
-
-var AriDecoder = // final FC[] fc = new FC[256];
-// byte[] R;
-function AriDecoder() {
-  (0, _classCallCheck2.default)(this, AriDecoder);
-  this.fc = new Array(256);
-
-  for (var i = 0; i < this.fc.length; i += 1) {
-    this.fc[i] = new FC();
-  }
-
-  this.R = null;
-};
-
-var _Symbol = // int start; // Start of range.
-// int freq; // Symbol frequency.
-function _Symbol() {
-  (0, _classCallCheck2.default)(this, _Symbol);
-  this.start = undefined;
-  this.freq = undefined;
-}; // Initialize a decoder symbol to start "start" and frequency "freq"
-
-
+Object.defineProperty(exports, "__esModule", { value: true });
+var errors_1 = require("../errors");
+var constants_1 = require("./constants");
+var FC = /** @class */ (function () {
+    // int F, C;
+    function FC() {
+        this.F = undefined;
+        this.C = undefined;
+    }
+    return FC;
+}());
+var AriDecoder = /** @class */ (function () {
+    // final FC[] fc = new FC[256];
+    // byte[] R;
+    function AriDecoder() {
+        this.fc = new Array(256);
+        for (var i = 0; i < this.fc.length; i += 1) {
+            this.fc[i] = new FC();
+        }
+        this.R = null;
+    }
+    return AriDecoder;
+}());
+var Symbol = /** @class */ (function () {
+    // int start; // Start of range.
+    // int freq; // Symbol frequency.
+    function Symbol() {
+        this.start = undefined;
+        this.freq = undefined;
+    }
+    return Symbol;
+}());
+// Initialize a decoder symbol to start "start" and frequency "freq"
 function symbolInit(sym, start, freq) {
-  if (!(start <= 1 << 16)) throw new CramMalformedError("assertion failed: start <= 1<<16");
-  if (!(freq <= (1 << 16) - start)) throw new CramMalformedError("assertion failed: freq <= 1<<16");
-  sym.start = start;
-  sym.freq = freq;
-} // Advances in the bit stream by "popping" a single symbol with range start
+    if (!(start <= 1 << 16)) {
+        throw new errors_1.CramMalformedError("assertion failed: start <= 1<<16");
+    }
+    if (!(freq <= (1 << 16) - start)) {
+        throw new errors_1.CramMalformedError("assertion failed: freq <= 1<<16");
+    }
+    sym.start = start;
+    sym.freq = freq;
+}
+// Advances in the bit stream by "popping" a single symbol with range start
 // "start" and frequency "freq". All frequencies are assumed to sum to
 // "1 << scaleBits".
 // No renormalization or output happens.
-
-/* private static int */
-
-
-function advanceStep(
-/* final int */
-r,
-/* final int */
-start,
-/* final int */
-freq,
-/* final int */
-scaleBits) {
-  /* final int */
-  var mask = (1 << scaleBits) - 1; // s, x = D(x)
-
-  return freq * (r >> scaleBits) + (r & mask) - start;
-} // Equivalent to RansDecAdvanceStep that takes a symbol.
-
-/* static int  */
-
-
-function advanceSymbolStep(
-/* final int */
-r,
-/* final RansDecSymbol */
-sym,
-/* final int */
-scaleBits) {
-  return advanceStep(r, sym.start, sym.freq, scaleBits);
-} // Returns the current cumulative frequency (map it to a symbol yourself!)
-
-/* static int */
-
-
-function get(
-/* final int */
-r,
-/* final int */
-scaleBits) {
-  return r & (1 << scaleBits) - 1;
-} // Advances in the bit stream by "popping" a single symbol with range start
+/* private static int */ function advanceStep(
+/* final int */ r, 
+/* final int */ start, 
+/* final int */ freq, 
+/* final int */ scaleBits) {
+    /* final int */ var mask = (1 << scaleBits) - 1;
+    // s, x = D(x)
+    return freq * (r >> scaleBits) + (r & mask) - start;
+}
+// Equivalent to RansDecAdvanceStep that takes a symbol.
+/* static int  */ function advanceSymbolStep(
+/* final int */ r, 
+/* final RansDecSymbol */ sym, 
+/* final int */ scaleBits) {
+    return advanceStep(r, sym.start, sym.freq, scaleBits);
+}
+// Returns the current cumulative frequency (map it to a symbol yourself!)
+/* static int */ function get(/* final int */ r, /* final int */ scaleBits) {
+    return r & ((1 << scaleBits) - 1);
+}
+// Advances in the bit stream by "popping" a single symbol with range start
 // "start" and frequency "freq". All frequencies are assumed to sum to
 // "1 << scaleBits",
 // and the resulting bytes get written to ptr (which is updated).
-
-/* private static int */
-
-
-function advance(
-/* int */
-r,
-/* final ByteBuffer */
-pptr,
-/* final int */
-start,
-/* final int */
-freq,
-/* final int */
-scaleBits) {
-  /* final int */
-  var mask = (1 << scaleBits) - 1; // s, x = D(x)
-
-  r = freq * (r >> scaleBits) + (r & mask) - start; // re-normalize
-
-  if (r < Constants.RANS_BYTE_L) {
-    do {
-      /* final int */
-      var b = 0xff & pptr.get();
-      r = r << 8 | b;
-    } while (r < Constants.RANS_BYTE_L);
-  }
-
-  return r;
-} // Equivalent to RansDecAdvance that takes a symbol.
-
-/*  static int */
-
-
-function advanceSymbol(
-/* final int */
-r,
-/* final ByteBuffer */
-pptr,
-/* final RansDecSymbol */
-sym,
-/* final int */
-scaleBits) {
-  return advance(r, pptr, sym.start, sym.freq, scaleBits);
-} // Re-normalize.
-
-/*  static int */
-
-
-function renormalize(
-/* int */
-r,
-/* final ByteBuffer */
-pptr) {
-  // re-normalize
-  if (r < Constants.RANS_BYTE_L) {
-    do {
-      r = r << 8 | 0xff & pptr.get();
-    } while (r < Constants.RANS_BYTE_L);
-  }
-
-  return r;
+/* private static int */ function advance(
+/* int */ r, 
+/* final ByteBuffer */ pptr, 
+/* final int */ start, 
+/* final int */ freq, 
+/* final int */ scaleBits) {
+    /* final int */ var mask = (1 << scaleBits) - 1;
+    // s, x = D(x)
+    r = freq * (r >> scaleBits) + (r & mask) - start;
+    // re-normalize
+    if (r < constants_1.RANS_BYTE_L) {
+        do {
+            /* final int */ var b = 0xff & pptr.get();
+            r = (r << 8) | b;
+        } while (r < constants_1.RANS_BYTE_L);
+    }
+    return r;
 }
-
+// Equivalent to RansDecAdvance that takes a symbol.
+/*  static int */ function advanceSymbol(
+/* final int */ r, 
+/* final ByteBuffer */ pptr, 
+/* final RansDecSymbol */ sym, 
+/* final int */ scaleBits) {
+    return advance(r, pptr, sym.start, sym.freq, scaleBits);
+}
+// Re-normalize.
+/*  static int */ function renormalize(
+/* int */ r, 
+/* final ByteBuffer */ pptr) {
+    // re-normalize
+    if (r < constants_1.RANS_BYTE_L) {
+        do {
+            r = (r << 8) | (0xff & pptr.get());
+        } while (r < constants_1.RANS_BYTE_L);
+    }
+    return r;
+}
 var Decode = {
-  FC: FC,
-  AriDecoder: AriDecoder,
-  Symbol: _Symbol,
-  symbolInit: symbolInit,
-  advanceStep: advanceStep,
-  advanceSymbolStep: advanceSymbolStep,
-  get: get,
-  advanceSymbol: advanceSymbol,
-  renormalize: renormalize
+    FC: FC,
+    AriDecoder: AriDecoder,
+    Symbol: Symbol,
+    symbolInit: symbolInit,
+    advanceStep: advanceStep,
+    advanceSymbolStep: advanceSymbolStep,
+    get: get,
+    advanceSymbol: advanceSymbol,
+    renormalize: renormalize,
 };
-module.exports = Decode;
+exports.default = Decode;
+//# sourceMappingURL=decoding.js.map

dist/rans/frequencies.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _fill = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/fill"));
-
-var _require = require('../errors'),
-    CramMalformedError = _require.CramMalformedError;
-
-var Constants = require('./constants');
-
-var Decoding = require('./decoding');
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.readStatsO1 = exports.readStatsO0 = void 0;
+var errors_1 = require("../errors");
+var constants_1 = require("./constants");
+var decoding_1 = __importDefault(require("./decoding"));
 function assert(result) {
-  if (!result) throw new CramMalformedError('assertion failed');
+    if (!result) {
+        throw new errors_1.CramMalformedError('assertion failed');
+    }
 }
-
 function readStatsO0(
-/* ByteBuffer */
-cp,
-/* Decoding.AriDecoder */
-decoder,
-/* Decoding.RansDecSymbol[] */
-syms) {
-  // Pre-compute reverse lookup of frequency.
-  var rle = 0;
-  var x = 0;
-  var j = cp.get() & 0xff;
-
-  do {
-    var _context;
-
-    if (decoder.fc[j] == null) decoder.fc[j] = new Decoding.FC();
-    decoder.fc[j].F = cp.get() & 0xff;
-
-    if (decoder.fc[j].F >= 128) {
-      decoder.fc[j].F &= ~128;
-      decoder.fc[j].F = (decoder.fc[j].F & 127) << 8 | cp.get() & 0xff;
-    }
-
-    decoder.fc[j].C = x;
-    Decoding.symbolInit(syms[j], decoder.fc[j].C, decoder.fc[j].F);
-    /* Build reverse lookup table */
-
-    if (!decoder.R) decoder.R = new Array(Constants.TOTFREQ);
-    (0, _fill.default)(_context = decoder.R).call(_context, j, x, x + decoder.fc[j].F);
-    x += decoder.fc[j].F;
-
-    if (rle === 0 && j + 1 === (0xff & cp.getByteAt(cp.position()))) {
-      j = cp.get() & 0xff;
-      rle = cp.get() & 0xff;
-    } else if (rle !== 0) {
-      rle -= 1;
-      j += 1;
-    } else {
-      j = cp.get() & 0xff;
-    }
-  } while (j !== 0);
-
-  assert(x < Constants.TOTFREQ);
-}
-
-function readStatsO1(
-/* ByteBuffer */
-cp,
-/*  Decoding.AriDecoder[] */
-D,
-/* Decoding.RansDecSymbol[][] */
-syms) {
-  var rlei = 0;
-  var i = 0xff & cp.get();
-
-  do {
-    var rlej = 0;
+/* ByteBuffer */ cp, 
+/* Decoding.AriDecoder */ decoder, 
+/* Decoding.RansDecSymbol[] */ syms) {
+    // Pre-compute reverse lookup of frequency.
+    var rle = 0;
     var x = 0;
-    var j = 0xff & cp.get();
-    if (D[i] == null) D[i] = new Decoding.AriDecoder();
-
+    var j = cp.get() & 0xff;
     do {
-      var _context2;
-
-      if (D[i].fc[j] == null) D[i].fc[j] = new Decoding.FC();
-      D[i].fc[j].F = 0xff & cp.get();
-
-      if (D[i].fc[j].F >= 128) {
-        D[i].fc[j].F &= ~128;
-        D[i].fc[j].F = (D[i].fc[j].F & 127) << 8 | 0xff & cp.get();
-      }
-
-      D[i].fc[j].C = x;
-      if (D[i].fc[j].F === 0) D[i].fc[j].F = Constants.TOTFREQ;
-      if (syms[i][j] == null) syms[i][j] = new Decoding.RansDecSymbol();
-      Decoding.symbolInit(syms[i][j], D[i].fc[j].C, D[i].fc[j].F);
-      /* Build reverse lookup table */
-
-      if (D[i].R == null) D[i].R = new Array(Constants.TOTFREQ);
-      (0, _fill.default)(_context2 = D[i].R).call(_context2, j, x, x + D[i].fc[j].F);
-      x += D[i].fc[j].F;
-      assert(x <= Constants.TOTFREQ);
-
-      if (rlej === 0 && j + 1 === (0xff & cp.getByteAt(cp.position()))) {
-        j = 0xff & cp.get();
-        rlej = 0xff & cp.get();
-      } else if (rlej !== 0) {
-        rlej -= 1;
-        j += 1;
-      } else {
-        j = 0xff & cp.get();
-      }
+        if (decoder.fc[j] == null) {
+            decoder.fc[j] = new decoding_1.default.FC();
+        }
+        decoder.fc[j].F = cp.get() & 0xff;
+        if (decoder.fc[j].F >= 128) {
+            decoder.fc[j].F &= ~128;
+            decoder.fc[j].F = ((decoder.fc[j].F & 127) << 8) | (cp.get() & 0xff);
+        }
+        decoder.fc[j].C = x;
+        decoding_1.default.symbolInit(syms[j], decoder.fc[j].C, decoder.fc[j].F);
+        /* Build reverse lookup table */
+        if (!decoder.R) {
+            decoder.R = new Array(constants_1.TOTFREQ);
+        }
+        decoder.R.fill(j, x, x + decoder.fc[j].F);
+        x += decoder.fc[j].F;
+        if (rle === 0 && j + 1 === (0xff & cp.getByteAt(cp.position()))) {
+            j = cp.get() & 0xff;
+            rle = cp.get() & 0xff;
+        }
+        else if (rle !== 0) {
+            rle -= 1;
+            j += 1;
+        }
+        else {
+            j = cp.get() & 0xff;
+        }
     } while (j !== 0);
-
-    if (rlei === 0 && i + 1 === (0xff & cp.getByteAt(cp.position()))) {
-      i = 0xff & cp.get();
-      rlei = 0xff & cp.get();
-    } else if (rlei !== 0) {
-      rlei -= 1;
-      i += 1;
-    } else {
-      i = 0xff & cp.get();
-    }
-  } while (i !== 0);
+    assert(x < constants_1.TOTFREQ);
 }
-
-module.exports = {
-  readStatsO0: readStatsO0,
-  readStatsO1: readStatsO1
-};
+exports.readStatsO0 = readStatsO0;
+function readStatsO1(
+/* ByteBuffer */ cp, 
+/*  Decoding.AriDecoder[] */ D, 
+/* Decoding.RansDecSymbol[][] */ syms) {
+    var rlei = 0;
+    var i = 0xff & cp.get();
+    do {
+        var rlej = 0;
+        var x = 0;
+        var j = 0xff & cp.get();
+        if (D[i] == null) {
+            D[i] = new decoding_1.default.AriDecoder();
+        }
+        do {
+            if (D[i].fc[j] == null) {
+                D[i].fc[j] = new decoding_1.default.FC();
+            }
+            D[i].fc[j].F = 0xff & cp.get();
+            if (D[i].fc[j].F >= 128) {
+                D[i].fc[j].F &= ~128;
+                D[i].fc[j].F = ((D[i].fc[j].F & 127) << 8) | (0xff & cp.get());
+            }
+            D[i].fc[j].C = x;
+            if (D[i].fc[j].F === 0) {
+                D[i].fc[j].F = constants_1.TOTFREQ;
+            }
+            if (syms[i][j] == null) {
+                syms[i][j] = new decoding_1.default.RansDecSymbol();
+            }
+            decoding_1.default.symbolInit(syms[i][j], D[i].fc[j].C, D[i].fc[j].F);
+            /* Build reverse lookup table */
+            if (D[i].R == null) {
+                D[i].R = new Array(constants_1.TOTFREQ);
+            }
+            D[i].R.fill(j, x, x + D[i].fc[j].F);
+            x += D[i].fc[j].F;
+            assert(x <= constants_1.TOTFREQ);
+            if (rlej === 0 && j + 1 === (0xff & cp.getByteAt(cp.position()))) {
+                j = 0xff & cp.get();
+                rlej = 0xff & cp.get();
+            }
+            else if (rlej !== 0) {
+                rlej -= 1;
+                j += 1;
+            }
+            else {
+                j = 0xff & cp.get();
+            }
+        } while (j !== 0);
+        if (rlei === 0 && i + 1 === (0xff & cp.getByteAt(cp.position()))) {
+            i = 0xff & cp.get();
+            rlei = 0xff & cp.get();
+        }
+        else if (rlei !== 0) {
+            rlei -= 1;
+            i += 1;
+        }
+        else {
+            i = 0xff & cp.get();
+        }
+    } while (i !== 0);
+}
+exports.readStatsO1 = readStatsO1;
+//# sourceMappingURL=frequencies.js.map

dist/rans/index.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _fill = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/fill"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/createClass"));
-
-var _require = require('../errors'),
-    CramMalformedError = _require.CramMalformedError;
-
-var Decoding = require('./decoding');
-
-var Frequencies = require('./frequencies');
-
-var D04 = require('./d04');
-
-var D14 = require('./d14'); // const /* int */ ORDER_BYTE_LENGTH = 1
+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 decoding_1 = __importDefault(require("./decoding"));
+var frequencies_1 = require("./frequencies");
+var d04_1 = __importDefault(require("./d04"));
+var d14_1 = __importDefault(require("./d14"));
+// const /* int */ ORDER_BYTE_LENGTH = 1
 // const /* int */ COMPRESSED_BYTE_LENGTH = 4
-
-
-var
-/* int */
-RAW_BYTE_LENGTH = 4; // const /* int */ PREFIX_BYTE_LENGTH =
+var /* int */ RAW_BYTE_LENGTH = 4;
+// const /* int */ PREFIX_BYTE_LENGTH =
 //   ORDER_BYTE_LENGTH + COMPRESSED_BYTE_LENGTH + RAW_BYTE_LENGTH
@@ -107,162 +95,111 @@ // enum ORDER {
 // }
-
-function
-/* static ByteBuffer */
-uncompressOrder0Way4(
-/* const ByteBuffer  */
-input,
-/* const ByteBuffer  */
-out) {
-  // input.order(ByteOrder.LITTLE_ENDIAN);
-  var D = new Decoding.AriDecoder();
-  var syms = new Array(256);
-
-  for (var i = 0; i < syms.length; i += 1) {
-    syms[i] = new Decoding.Symbol();
-  }
-
-  Frequencies.readStatsO0(input, D, syms);
-  D04.uncompress(input, D, syms, out);
-  return out;
+function uncompressOrder0Way4(
+/* const ByteBuffer  */ input, 
+/* const ByteBuffer  */ out) {
+    // input.order(ByteOrder.LITTLE_ENDIAN);
+    var D = new decoding_1.default.AriDecoder();
+    var syms = new Array(256);
+    for (var i = 0; i < syms.length; i += 1) {
+        syms[i] = new decoding_1.default.Symbol();
+    }
+    (0, frequencies_1.readStatsO0)(input, D, syms);
+    (0, d04_1.default)(input, D, syms, out);
+    return out;
 }
-
-function
-/* static ByteBuffer */
-uncompressOrder1Way4(
-/* const ByteBuffer */
-input,
-/* const ByteBuffer */
-output) {
-  var D = new Array(256);
-
-  for (var i = 0; i < D.length; i += 1) {
-    D[i] = new Decoding.AriDecoder();
-  }
-
-  var
-  /* Decoding.RansDecSymbol[][]  */
-  syms = new Array(256);
-
-  for (var _i = 0; _i < syms.length; _i += 1) {
-    syms[_i] = new Array(256);
-
-    for (var j = 0; j < syms[_i].length; j += 1) {
-      syms[_i][j] = new Decoding.Symbol();
+function uncompressOrder1Way4(
+/* const ByteBuffer */ input, 
+/* const ByteBuffer */ output) {
+    var D = new Array(256);
+    for (var i = 0; i < D.length; i += 1) {
+        D[i] = new decoding_1.default.AriDecoder();
     }
-  }
-
-  Frequencies.readStatsO1(input, D, syms);
-  D14.uncompress(input, output, D, syms);
-  return output;
+    var /* Decoding.RansDecSymbol[][]  */ syms = new Array(256);
+    for (var i = 0; i < syms.length; i += 1) {
+        syms[i] = new Array(256);
+        for (var j = 0; j < syms[i].length; j += 1) {
+            syms[i][j] = new decoding_1.default.Symbol();
+        }
+    }
+    (0, frequencies_1.readStatsO1)(input, D, syms);
+    (0, d14_1.default)(input, output, D, syms);
+    return output;
 }
 /* compat layer to make a node buffer act like a java ByteBuffer */
-
-
-var ByteBuffer =
-/*#__PURE__*/
-function () {
-  function ByteBuffer(nodeBuffer) {
-    var initialInputPosition = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : 0;
-    (0, _classCallCheck2.default)(this, ByteBuffer);
-    this._buffer = nodeBuffer;
-    this._position = initialInputPosition;
-    this.length = nodeBuffer.length;
-  }
-
-  (0, _createClass2.default)(ByteBuffer, [{
-    key: "get",
-    value: function get() {
-      var b = this._buffer[this._position];
-      this._position += 1;
-      return b;
+var ByteBuffer = /** @class */ (function () {
+    function ByteBuffer(nodeBuffer, initialInputPosition) {
+        if (initialInputPosition === void 0) { initialInputPosition = 0; }
+        this._buffer = nodeBuffer;
+        this._position = initialInputPosition;
+        this.length = nodeBuffer.length;
     }
-  }, {
-    key: "getByte",
-    value: function getByte() {
-      return this.get();
+    ByteBuffer.prototype.get = function () {
+        var b = this._buffer[this._position];
+        this._position += 1;
+        return b;
+    };
+    ByteBuffer.prototype.getByte = function () {
+        return this.get();
+    };
+    ByteBuffer.prototype.getByteAt = function (position) {
+        return this._buffer[position];
+    };
+    ByteBuffer.prototype.position = function () {
+        return this._position;
+    };
+    ByteBuffer.prototype.put = function (val) {
+        this._buffer[this._position] = val;
+        this._position += 1;
+        return val;
+    };
+    ByteBuffer.prototype.putAt = function (position, val) {
+        this._buffer[position] = val;
+        return val;
+    };
+    ByteBuffer.prototype.setPosition = function (pos) {
+        this._position = pos;
+        return pos;
+    };
+    ByteBuffer.prototype.getInt = function () {
+        var i = this._buffer.readInt32LE(this._position);
+        this._position += 4;
+        return i;
+    };
+    ByteBuffer.prototype.remaining = function () {
+        return this._buffer.length - this._position;
+    };
+    return ByteBuffer;
+}());
+// static /* const */ ByteBuffer EMPTY_BUFFER = ByteBuffer.allocate(0);
+function uncompress(inputBuffer, outputBuffer, initialInputPosition) {
+    if (initialInputPosition === void 0) { initialInputPosition = 0; }
+    if (inputBuffer.length === 0) {
+        outputBuffer.fill(0);
+        return outputBuffer;
     }
-  }, {
-    key: "getByteAt",
-    value: function getByteAt(position) {
-      return this._buffer[position];
+    var input = new ByteBuffer(inputBuffer, initialInputPosition);
+    // input.order(ByteOrder.LITTLE_ENDIAN);
+    var order = input.get();
+    if (order !== 0 && order !== 1) {
+        throw new errors_1.CramMalformedError("Invalid rANS order ".concat(order));
     }
-  }, {
-    key: "position",
-    value: function position() {
-      return this._position;
+    var /* int */ inputSize = input.getInt();
+    if (inputSize !== input.remaining() - RAW_BYTE_LENGTH) {
+        throw new errors_1.CramMalformedError('Incorrect input length.');
     }
-  }, {
-    key: "put",
-    value: function put(val) {
-      this._buffer[this._position] = val;
-      this._position += 1;
-      return val;
+    var /* int */ outputSize = input.getInt();
+    var output = new ByteBuffer(outputBuffer || Buffer.allocUnsafe(outputSize));
+    // TODO output.limit(outputSize)
+    if (output.length < outputSize) {
+        throw new errors_1.CramMalformedError("Output buffer too small to fit ".concat(outputSize, " bytes."));
     }
-  }, {
-    key: "putAt",
-    value: function putAt(position, val) {
-      this._buffer[position] = val;
-      return val;
+    switch (order) {
+        case 0:
+            return uncompressOrder0Way4(input, output);
+        case 1:
+            return uncompressOrder1Way4(input, output);
+        default:
+            throw new errors_1.CramMalformedError("Invalid rANS order: ".concat(order));
     }
-  }, {
-    key: "setPosition",
-    value: function setPosition(pos) {
-      this._position = pos;
-      return pos;
-    }
-  }, {
-    key: "getInt",
-    value: function getInt() {
-      var i = this._buffer.readInt32LE(this._position);
-
-      this._position += 4;
-      return i;
-    }
-  }, {
-    key: "remaining",
-    value: function remaining() {
-      return this._buffer.length - this._position;
-    }
-  }]);
-  return ByteBuffer;
-}(); // static /* const */ ByteBuffer EMPTY_BUFFER = ByteBuffer.allocate(0);
-
-
-function uncompress(inputBuffer, outputBuffer) {
-  var initialInputPosition = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : 0;
-
-  if (inputBuffer.length === 0) {
-    (0, _fill.default)(outputBuffer).call(outputBuffer, 0);
-    return outputBuffer;
-  }
-
-  var input = new ByteBuffer(inputBuffer, initialInputPosition); // input.order(ByteOrder.LITTLE_ENDIAN);
-
-  var order = input.get();
-  if (order !== 0 && order !== 1) throw new CramMalformedError("Invalid rANS order ".concat(order));
-  var
-  /* int */
-  inputSize = input.getInt();
-  if (inputSize !== input.remaining() - RAW_BYTE_LENGTH) throw new CramMalformedError('Incorrect input length.');
-  var
-  /* int */
-  outputSize = input.getInt();
-  var output = new ByteBuffer(outputBuffer || Buffer.allocUnsafe(outputSize)); // TODO output.limit(outputSize)
-
-  if (output.length < outputSize) throw new CramMalformedError("Output buffer too small to fit ".concat(outputSize, " bytes."));
-
-  switch (order) {
-    case 0:
-      return uncompressOrder0Way4(input, output);
-
-    case 1:
-      return uncompressOrder1Way4(input, output);
-
-    default:
-      throw new CramMalformedError("Invalid rANS order: ".concat(order));
-  }
 }
-
-module.exports = {
-  uncompress: uncompress
-};
+exports.default = uncompress;
+//# sourceMappingURL=index.js.map

dist/sam.js

 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/slicedToArray"));
-
-var _map = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/map"));
-
-var _slice = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/slice"));
-
-var _toArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/toArray"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseHeaderText = void 0;
 function parseHeaderText(text) {
-  var lines = text.split(/\r?\n/);
-  var data = [];
-  (0, _forEach.default)(lines).call(lines, function (line) {
-    var _line$split = line.split(/\t/),
-        _line$split2 = (0, _toArray2.default)(_line$split),
-        tag = _line$split2[0],
-        fields = (0, _slice.default)(_line$split2).call(_line$split2, 1);
-
-    var parsedFields = (0, _map.default)(fields).call(fields, function (f) {
-      var _f$split = f.split(':', 2),
-          _f$split2 = (0, _slicedToArray2.default)(_f$split, 2),
-          fieldTag = _f$split2[0],
-          value = _f$split2[1];
-
-      return {
-        tag: fieldTag,
-        value: value
-      };
+    var lines = text.split(/\r?\n/);
+    var data = [];
+    lines.forEach(function (line) {
+        var _a = line.split(/\t/), tag = _a[0], fields = _a.slice(1);
+        var parsedFields = fields.map(function (f) {
+            var _a = f.split(':', 2), fieldTag = _a[0], value = _a[1];
+            return { tag: fieldTag, value: value };
+        });
+        if (tag) {
+            data.push({ tag: tag.substr(1), data: parsedFields });
+        }
     });
-    if (tag) data.push({
-      tag: tag.substr(1),
-      data: parsedFields
-    });
-  });
-  return data;
+    return data;
 }
-
-module.exports = {
-  parseHeaderText: parseHeaderText
-};
+exports.parseHeaderText = parseHeaderText;
+//# sourceMappingURL=sam.js.map

errors.js

 "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.json

 {
   "name": "@gmod/cram",
-  "version": "1.5.9",
+  "version": "1.6.0",
   "description": "read CRAM files with pure Javascript",
@@ -8,2 +8,3 @@ "license": "MIT",
   "main": "dist/index.js",
+  "module": "esm/index.js",
   "author": {
@@ -19,23 +20,19 @@ "name": "Robert Buels",
     "errors.js",
-    "dist"
+    "dist",
+    "esm"
   ],
   "scripts": {
-    "test": "node ./node_modules/.bin/mocha",
-    "coverage": "rm -rf coverage; nyc ./node_modules/.bin/mocha; nyc report --reporter=lcov",
+    "test": "jest",
     "lint": "eslint src test",
     "docs": "documentation readme --shallow src/indexedCramFile.js --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.js --section=CramFile; documentation readme --shallow src/craiIndex.js --section=CraiIndex;  documentation readme --shallow errors.js '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.js --section=CramFile; documentation readme --shallow src/cramFile/record.js --section=CramRecord",
-    "clean": "rimraf dist",
     "prebuild": "npm run clean",
-    "build": "babel src -d dist && webpack",
-    "built-tests": "rm -rf built-tests; mkdir built-tests; ln -s ../test/data built-tests/data; babel test/*.js -d built-tests; babel test/lib/*.js -d built-tests/lib;babel test/lib/fasta/*.js -d built-tests/lib/fasta;node ./node_modules/.bin/mocha built-tests",
-    "watch": "npm-watch",
+    "clean": "rimraf dist esm",
+    "build:esm": "tsc --target es2018 --outDir esm",
+    "build:es5": "tsc --target es5 --outDir dist",
+    "build": "npm run build:esm && npm run build:es5",
+    "postbuild": "webpack",
     "prepublishOnly": "npm test && npm run build && cp dist/errors.js errors.js",
     "postpublish": "rm errors.js",
-    "postversion": "git push origin master --follow-tags"
+    "postversion": "git push --follow-tags"
   },
-  "watch": {
-    "test": "{src,test}/*.js",
-    "lint": "{src,test}/*.js",
-    "build": "src"
-  },
   "keywords": [
@@ -48,6 +45,7 @@ "cram",
   "dependencies": {
-    "@babel/runtime-corejs3": "^7.4.5",
     "@gmod/binary-parser": "^1.3.5",
+    "@jkbonfield/htscodecs": "^0.5.1",
     "abortable-promise-cache": "^1.2.0",
     "buffer-crc32": "^0.2.13",
+    "bzip2": "^0.1.1",
     "cross-fetch": "^3.0.0",
@@ -60,22 +58,18 @@ "es6-promisify": "^6.0.1",
   "devDependencies": {
-    "@babel/cli": "^7.4.4",
-    "@babel/core": "^7.4.5",
-    "@babel/plugin-transform-runtime": "^7.4.4",
-    "@babel/preset-env": "^7.4.5",
-    "chai": "^4.1.2",
-    "documentation": "^9.1.1",
-    "eslint": "^5.12.0",
-    "eslint-config-airbnb-base": "^13.1.0",
-    "eslint-config-prettier": "^4.1.0",
-    "eslint-plugin-import": "^2.2.0",
-    "eslint-plugin-prettier": "^3.0.1",
-    "get-stream": "^4.1.0",
-    "glob": "^7.1.2",
-    "imports-loader": "^0.8.0",
-    "mocha": "^6.0.0",
-    "mock-fs": "^4.12.0",
-    "npm-watch": "^0.5.0",
-    "nyc": "^13.0.0",
-    "prettier": "^1.10.2",
-    "rimraf": "^2.6.1",
+    "@gmod/indexedfasta": "^2.0.2",
+    "@types/jest": "^27.4.0",
+    "@typescript-eslint/eslint-plugin": "^5.9.1",
+    "@typescript-eslint/parser": "^5.9.1",
+    "documentation": "^13.2.5",
+    "eslint": "^7.0.0",
+    "eslint-config-prettier": "^8.3.0",
+    "eslint-plugin-import": "^2.25.4",
+    "eslint-plugin-prettier": "^4.0.0",
+    "glob": "^7.2.0",
+    "jest": "^27.4.7",
+    "mock-fs": "^5.1.2",
+    "prettier": "^2.5.1",
+    "rimraf": "^3.0.2",
+    "ts-jest": "^27.1.2",
+    "typescript": "^4.5.4",
     "webpack": "4",
@@ -86,3 +80,7 @@ "webpack-cli": "^3.2.1"
     "access": "public"
+  },
+  "browser": {
+    "./dist/io/localFile.js": false,
+    "./esm/io/localFile.js": false
   }
 }

README.md

 # @gmod/cram
 
-[![Generated with nod](https://img.shields.io/badge/generator-nod-2196F3.svg?style=flat-square)](https://github.com/diegohaz/nod)
 [![NPM version](https://img.shields.io/npm/v/@gmod/cram.svg?style=flat-square)](https://npmjs.org/package/@gmod/cram)
-[![Build Status](https://img.shields.io/travis/GMOD/cram-js/master.svg?style=flat-square)](https://travis-ci.org/GMOD/cram-js) [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/cram-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/cram-js/branch/master) [![Greenkeeper badge](https://badges.greenkeeper.io/GMOD/cram-js.svg)](https://greenkeeper.io/)
+[![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/cram-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/cram-js/branch/master)
+[![Build Status](https://img.shields.io/github/workflow/status/GMOD/cram-js/Push/master?logo=github\&style=flat-query)](https://github.com/GMOD/cram-js/actions?query=branch%3Amaster+workflow%3APush+)
 
 Read CRAM files (indexed or unindexed) with pure JS, works in node or in the browser.
 
--   Reads CRAM 3.x and 2.x
--   Does not read CRAM 1.x
--   Can use .crai indexes out of the box, for efficient sequence fetching, but also has an [index API](#craiindex) that would allow use with other index types
--   Does not implement bzip2 or lzma codecs (yet), as these are rarely used in-the-wild; if this is important to your use case, please file an issue
+*   Reads CRAM 3.x and 2.x (3.1 included)
+*   Does not read CRAM 1.x
+*   Can use .crai indexes out of the box, for efficient sequence fetching, but also has an [index API](#craiindex) that would allow use with other index types
+*   Does not implement bzip2 or lzma codecs (yet), as these are rarely used in-the-wild; if this is important to your use case, please file an issue
 
@@ -41,3 +41,3 @@ ## Install
   index: new CraiIndex({
-    path: '/filesystem/yourfile.cram.crai'),
+    path: '/filesystem/yourfile.cram.crai',
   }),
@@ -49,4 +49,4 @@ seqFetch: async (seqId, start, end) => {
     // * the seqId is a numeric identifier
+    // * you can return an empty string for testing if you want, but you may not get proper interpretation of record.readFeatures
     return t.getSequence(seqId, start-1, end)
-    }
   },
@@ -65,12 +65,15 @@ checkSequenceMD5: false,
     console.log(`got a record named ${record.readName}`)
-    record.readFeatures.forEach(({ code, pos, refPos, ref, sub }) => {
-      // process the "read features". this can be used similar to
-      // CIGAR/MD strings in SAM. see CRAM specs for more details.
-      if (code === 'X')
-        console.log(
-          `${
-            record.readName
-          } shows a base substitution of ${ref}->${sub} at ${refPos}`,
-        )
-    })
+    if(record.readFeatures != undefined) {
+      record.readFeatures.forEach(({ code, pos, refPos, ref, sub }) => {
+        // process the read features. this can be used similar to
+        // CIGAR/MD strings in SAM. see CRAM specs for more details.
+        if (code === 'X') {
+          console.log(
+            `${
+              record.readName
+            } shows a base substitution of ${ref}->${sub} at ${refPos}`,
+          )
+        }
+      })
+    }
   })
@@ -88,39 +91,40 @@ }
 
--   [CramRecord](#cramrecord) - format of CRAM records returned by this API
-     - [ReadFeatures](#readfeatures) - format of read features on records
--   [IndexedCramFile](#indexedcramfile) - indexed access into a CRAM file
--   [CramFile](#cramfile) - .cram API
--   [CraiIndex](#craiindex) - .crai index API
--   [Error Classes](#error-classes) - special error classes thrown by this API
+*   [CramRecord](#cramrecord) - format of CRAM records returned by this API
+    *   [ReadFeatures](#readfeatures) - format of read features on records
+*   [IndexedCramFile](#indexedcramfile) - indexed access into a CRAM file
+*   [CramFile](#cramfile) - .cram API
+*   [CraiIndex](#craiindex) - .crai index API
+*   [Error Classes](#error-classes) - special error classes thrown by this API
 
 ### CramRecord
 
-These are the record objects returned by this API. Much of the data
-is stored in them as simple object entries, but there are some accessor
-methods used for conveniently getting the values of each of the flags in
-the `flags` and `cramFlags` fields.
+<!-- Generated by documentation.js. Update this documentation by updating the source code. -->
 
-#### Static fields
+##### Table of Contents
 
-- **flags** (`number`): the SAM bit-flags field, see the SAM spec for interpretation. Some of the `is*` methods below interpret this field.
-- **cramFlags** (`number`): the CRAM-specific bit-flags field, see the CRAM spec for interpretation. Some of the `is*` methods below interpret this field.
-- **sequenceId** (`number`): the ID number of the record's reference sequence
-- **readLength** (`number`): length of the read in bases
-- **alignmentStart** (`number`): start coordinate of the alignment on the reference in 1-based closed coordinates
-- **readGroupId** (`number`): ID number of the read group, or -1 if none
-- **readName** (`number`): name of the read (string)
-- **templateSize** (`number`): for paired sequencing, the total size of the template
-- **readFeatures** (`array[ReadFeature]`): array of read features showing insertions, deletions, mismatches, etc. See [ReadFeatures](#readfeatures) for their format.
-- **lengthOnRef** (`number`): span of the alignment along the reference sequence
-- **mappingQuality** (`number`): SAM mapping quality
-- **qualityScores** (`array[number]`): array of numeric quality scores
-- **uniqueId** (`number`): unique ID number of the record within the file
-- **mate** (`object`)
-  - **flags** (`number`): CRAM mapping flags for the mate. See CRAM spec for interpretation. Some of the `is*` methods below interpret this field.
-  - **sequenceId** (`number`): reference sequence ID for the mate mapping
-  - **alignmentStart** (`number`): start coordinate of the mate mapping. 1-based coordinates.
+*   [CramRecord](#cramrecord)
+    *   [isPaired](#ispaired)
+    *   [isProperlyPaired](#isproperlypaired)
+    *   [isSegmentUnmapped](#issegmentunmapped)
+    *   [isMateUnmapped](#ismateunmapped)
+    *   [isReverseComplemented](#isreversecomplemented)
+    *   [isMateReverseComplemented](#ismatereversecomplemented)
+    *   [isRead1](#isread1)
+    *   [isRead2](#isread2)
+    *   [isSecondary](#issecondary)
+    *   [isFailedQc](#isfailedqc)
+    *   [isDuplicate](#isduplicate)
+    *   [isSupplementary](#issupplementary)
+    *   [isDetached](#isdetached)
+    *   [hasMateDownStream](#hasmatedownstream)
+    *   [isPreservingQualityScores](#ispreservingqualityscores)
+    *   [isUnknownBases](#isunknownbases)
+    *   [getReadBases](#getreadbases)
+    *   [getPairOrientation](#getpairorientation)
+    *   [addReferenceSequence](#addreferencesequence)
+        *   [Parameters](#parameters)
 
-<!-- Generated by documentation.js. Update this documentation by updating the source code. -->
+#### CramRecord
 
-#### Methods
+Class of each CRAM record returned by this API.
 
@@ -197,2 +201,8 @@ ##### isPaired
 
+##### getPairOrientation
+
+Get the pair orientation of a paired read. Adapted from igv.js
+
+Returns **[String](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** of paired orientatin
+
 ##### addReferenceSequence
@@ -205,10 +215,11 @@
 
-**Parameters**
+###### Parameters
 
--   `refRegion` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
-    -   `refRegion.start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
-    -   `refRegion.end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
-    -   `refRegion.seq` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** 
--   `compressionScheme` **CramContainerCompressionScheme** 
+*   `refRegion` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
 
+    *   `refRegion.start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
+    *   `refRegion.end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
+    *   `refRegion.seq` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** 
+*   `compressionScheme` **CramContainerCompressionScheme** 
+
 Returns **[undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined)** nothing
@@ -222,11 +233,9 @@
 
-- **code** (`character`): One of "bqBXIDiQNSPH". See page 15 of the CRAM v3 spec for their meanings.
-- **data** (`any`): the data associated with the feature. The format of this varies depending on the feature code.
-- **pos** (`number`): location relative to the read (1-based)
-- **refPos** (`number`): location relative to the reference (1-based)
+*   **code** (`character`): One of "bqBXIDiQNSPH". See page 15 of the CRAM v3 spec for their meanings.
+*   **data** (`any`): the data associated with the feature. The format of this varies depending on the feature code.
+*   **pos** (`number`): location relative to the read (1-based)
+*   **refPos** (`number`): location relative to the reference (1-based)
 
 ### IndexedCramFile
 
-The pairing of an index and a CramFile. Supports efficient fetching of records for sections of reference sequences.
-
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
@@ -236,16 +245,20 @@
 
--   [constructor](#constructor)
--   [getRecordsForRange](#getrecordsforrange)
--   [hasDataForReferenceSequence](#hasdataforreferencesequence)
+*   [constructor](#constructor)
+    *   [Parameters](#parameters)
+*   [getRecordsForRange](#getrecordsforrange)
+    *   [Parameters](#parameters-1)
+*   [hasDataForReferenceSequence](#hasdataforreferencesequence)
+    *   [Parameters](#parameters-2)
 
 #### constructor
 
-**Parameters**
+##### Parameters
 
--   `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
-    -   `args.cram` **CramFile** 
-    -   `args.index` **Index-like** object that supports getEntriesForRange(seqId,start,end) -> Promise\[Array[index entries]]
-    -   `args.cacheSize` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of CRAM records to cache.  default 20,000
-    -   `args.fetchSizeLimit` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of bytes to fetch in a single getRecordsForRange call.  Default 3 MiB.
-    -   `args.checkSequenceMD5` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** default true. if false, disables verifying the MD5
+*   `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
+
+    *   `args.cram` **CramFile**
+    *   `args.index` **Index-like** object that supports getEntriesForRange(seqId,start,end) -> Promise\[Array\[index entries]]
+    *   `args.cacheSize` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of CRAM records to cache.  default 20,000
+    *   `args.fetchSizeLimit` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of bytes to fetch in a single getRecordsForRange call.  Default 3 MiB.
+    *   `args.checkSequenceMD5` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** default true. if false, disables verifying the MD5
         checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
@@ -255,13 +268,14 @@
 
-**Parameters**
+##### Parameters
 
--   `seq` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** numeric ID of the reference sequence
--   `start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** start of the range of interest. 1-based closed coordinates.
--   `end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** end of the range of interest. 1-based closed coordinates.
+*   `seq` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** numeric ID of the reference sequence
+*   `start` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** start of the range of interest. 1-based closed coordinates.
+*   `end` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** end of the range of interest. 1-based closed coordinates.
+*   `opts`   (optional, default `{}`)
 
 #### hasDataForReferenceSequence
 
-**Parameters**
+##### Parameters
 
--   `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
+*   `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
 
@@ -277,18 +291,20 @@ Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** true if the CRAM file contains data for the given
 
--   [constructor](#constructor)
--   [containerCount](#containercount)
+*   [constructor](#constructor)
+    *   [Parameters](#parameters)
+*   [containerCount](#containercount)
 
 #### constructor
 
-**Parameters**
+##### Parameters
 
--   `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
-    -   `args.filehandle` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** a filehandle that implements the stat() and
+*   `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
+
+    *   `args.filehandle` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** a filehandle that implements the stat() and
         read() methods of the Node filehandle API <https://nodejs.org/api/fs.html#fs_class_filehandle>
-    -   `args.path` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** path to the cram file
-    -   `args.url` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** url for the cram file.  also supports file:// urls for local files
-    -   `args.seqFetch` **[function](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/function)?** a function with signature
+    *   `args.path` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** path to the cram file
+    *   `args.url` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?** url for the cram file.  also supports file:// urls for local files
+    *   `args.seqFetch` **[function](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/function)?** a function with signature
         `(seqId, startCoordinate, endCoordinate)` that returns a promise for a string of sequence bases
-    -   `args.cacheSize` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of CRAM records to cache.  default 20,000
-    -   `args.checkSequenceMD5` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** default true. if false, disables verifying the MD5
+    *   `args.cacheSize` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?** optional maximum number of CRAM records to cache.  default 20,000
+    *   `args.checkSequenceMD5` **[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?** default true. if false, disables verifying the MD5
         checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
@@ -298,8 +314,4 @@
 
-Returns **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** the number of containers in the file
-
 ### CraiIndex
 
-Represents a .crai index.
-
 <!-- Generated by documentation.js. Update this documentation by updating the source code. -->
@@ -309,20 +321,24 @@
 
--   [constructor](#constructor)
--   [hasDataForReferenceSequence](#hasdataforreferencesequence)
--   [getEntriesForRange](#getentriesforrange)
+*   [constructor](#constructor)
+    *   [Parameters](#parameters)
+*   [hasDataForReferenceSequence](#hasdataforreferencesequence)
+    *   [Parameters](#parameters-1)
+*   [getEntriesForRange](#getentriesforrange)
+    *   [Parameters](#parameters-2)
 
 #### constructor
 
-**Parameters**
+##### Parameters
 
--   `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
-    -   `args.path` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** 
-    -   `args.url` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** 
-    -   `args.filehandle` **FileHandle?** 
+*   `args` **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
 
+    *   `args.path` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**
+    *   `args.url` **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**
+    *   `args.filehandle` **FileHandle?**
+
 #### hasDataForReferenceSequence
 
-**Parameters**
+##### Parameters
 
--   `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
+*   `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
 
@@ -336,7 +352,7 @@ Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** true if the index contains entries for
 
-**Parameters**
+##### Parameters
 
--   `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
--   `queryStart` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
--   `queryEnd` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
+*   `seqId` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+*   `queryStart` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+*   `queryEnd` **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
 
@@ -347,46 +363,2 @@ Returns **[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)** promise for
 
-#### Error Classes
-
-`@gmod/cram/errors` contains some special error classes thrown by cram-js. A list of the error classes is below.
-
-<!-- Generated by documentation.js. Update this documentation by updating the source code. -->
-
-##### Table of Contents
-
--   [CramUnimplementedError](#cramunimplementederror)
--   [CramMalformedError](#crammalformederror)
--   [CramBufferOverrunError](#crambufferoverrunerror)
--   [CramSizeLimitError](#cramsizelimiterror)
--   [CramArgumentError](#cramargumenterror)
-
-#### CramUnimplementedError
-
-**Extends Error**
-
-Error caused by encountering a part of the CRAM spec that has not yet been implemented
-
-#### CramMalformedError
-
-**Extends CramError**
-
-An error caused by malformed data.
-
-#### CramBufferOverrunError
-
-**Extends CramMalformedError**
-
-An error caused by attempting to read beyond the end of the defined data.
-
-#### CramSizeLimitError
-
-**Extends CramError**
-
-An error caused by data being too big, exceeding a size limit.
-
-#### CramArgumentError
-
-**Extends CramError**
-
-An invalid argument was supplied to a cram-js method or object.
-
 ### CramUnimplementedError
@@ -393,0 +365,0 @@

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Filesystem access

Supply chain risk

Accesses the file system, and could potentially read sensitive data.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

950849

increased by67.41%

Dev dependency count

18

decreased by-18.18%

Number of package files

210

increased by438.46%

Lines of code

9970

increased by62.88%

Worsened metrics

Dependency count

10

increased by11.11%

Number of lines in readme file

375

decreased by-6.95%

Number of low supply chain risk alerts

3

increased by50%

Number of medium supply chain risk alerts

7

increased by75%

Dependency changes

• + Added@jkbonfield/htscodecs@^0.5.1

• + Addedbzip2@^0.1.1

• + Added@jkbonfield/htscodecs@0.5.1(transitive)

• + Addedbzip2@0.1.1(transitive)

• - Removed@babel/runtime-corejs3@^7.4.5

• - Removed@babel/runtime-corejs3@7.26.0(transitive)

• - Removedcore-js-pure@3.39.0(transitive)

• - Removedregenerator-runtime@0.14.1(transitive)