@gmod/cram 1.5.6 → 1.6.0

package/dist/indexedCramFile.d.ts

@@ -0,0 +1,39 @@
+export default class IndexedCramFile {
+    /**
+     *
+     * @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.
+     */
+    constructor(args: {
+        cram: CramFile;
+    });
+    cram: CramFile;
+    index: any;
+    fetchSizeLimit: any;
+    /**
+     *
+     * @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]]}
+     */
+    getRecordsForRange(seq: number, start: number, end: number, opts?: {}): Promise<any>[any[][CramRecord]];
+    getRecordsInSlice({ containerStart, sliceStart, sliceBytes }: {
+        containerStart: any;
+        sliceStart: any;
+        sliceBytes: any;
+    }, filterFunction: any): Promise<any>;
+    /**
+     *
+     * @param {number} seqId
+     * @returns {Promise} true if the CRAM file contains data for the given
+     * reference sequence numerical ID
+     */
+    hasDataForReferenceSequence(seqId: number): Promise<any>;
+}
+import CramFile from "./cramFile";

package/dist/indexedCramFile.js

@@ -1,325 +1,223 @@
 "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
      * @returns {Promise} true if the CRAM file contains data for the given
      * reference sequence numerical ID
      */
-
-  }, {
-    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

package/dist/indexedCramFile.js.map

@@ -0,0 +1 @@
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package/dist/io/bufferCache.d.ts

@@ -0,0 +1,12 @@
+export default class BufferCache {
+    constructor({ fetch, size, chunkSize }: {
+        fetch: any;
+        size?: number | undefined;
+        chunkSize?: number | undefined;
+    });
+    fetch: any;
+    chunkSize: number;
+    lruCache: any;
+    get(outputBuffer: any, offset: any, length: any, position: any): Promise<void>;
+    _getChunk(chunkNumber: any): any;
+}