@jbrowse/plugin-bed 1.7.10 → 2.0.1

package/dist/BigBedAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BigBedAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}

package/dist/index.js

@@ -1,137 +1,140 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+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 __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
 });
-exports.default = void 0;
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
-
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
-
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-
-var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
-
-var _BigBedAdapter = require("./BigBedAdapter");
-
-var _BedTabixAdapter = require("./BedTabixAdapter");
-
-var _tracks = require("@jbrowse/core/util/tracks");
-
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
-function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
-
-function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
-
-var BedPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(BedPlugin, _Plugin);
-
-  var _super = _createSuper(BedPlugin);
-
-  function BedPlugin() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, BedPlugin);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+var BigBedAdapter_1 = require("./BigBedAdapter");
+var BedTabixAdapter_1 = require("./BedTabixAdapter");
+var BedAdapter_1 = require("./BedAdapter");
+var tracks_1 = require("@jbrowse/core/util/tracks");
+var BedPlugin = /** @class */ (function (_super) {
+    __extends(BedPlugin, _super);
+    function BedPlugin() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.name = 'BedPlugin';
+        return _this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'BedPlugin');
-    return _this;
-  }
-
-  (0, _createClass2.default)(BedPlugin, [{
-    key: "install",
-    value: function install(pluginManager) {
-      pluginManager.addAdapterType(function () {
-        return new _AdapterType.default({
-          name: 'BigBedAdapter',
-          configSchema: _BigBedAdapter.configSchema,
-          getAdapterClass: function getAdapterClass() {
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('./BigBedAdapter/BigBedAdapter'));
-            }).then(function (r) {
-              return r.default;
+    BedPlugin.prototype.install = function (pluginManager) {
+        pluginManager.addAdapterType(function () {
+            return new AdapterType_1.default({
+                name: 'BigBedAdapter',
+                configSchema: BigBedAdapter_1.configSchema,
+                getAdapterClass: function () {
+                    return Promise.resolve().then(function () { return __importStar(require('./BigBedAdapter/BigBedAdapter')); }).then(function (r) { return r.default; });
+                },
+            });
+        });
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+            return function (file, index, adapterHint) {
+                var regexGuess = /\.(bb|bigbed)$/i;
+                var adapterName = 'BigBedAdapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                var obj = {
+                    type: adapterName,
+                    bigBedLocation: file,
+                };
+                if (regexGuess.test(fileName) && !adapterHint) {
+                    return obj;
+                }
+                else if (adapterHint === adapterName) {
+                    return obj;
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+        pluginManager.addAdapterType(function () {
+            return new AdapterType_1.default({
+                name: 'BedTabixAdapter',
+                configSchema: BedTabixAdapter_1.configSchema,
+                getAdapterClass: function () {
+                    return Promise.resolve().then(function () { return __importStar(require('./BedTabixAdapter/BedTabixAdapter')); }).then(function (r) { return r.default; });
+                },
             });
-          }
         });
-      });
-      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-        return function (file, index, adapterHint) {
-          var regexGuess = /\.(bb|bigbed)$/i;
-          var adapterName = 'BigBedAdapter';
-          var fileName = (0, _tracks.getFileName)(file);
-          var obj = {
-            type: adapterName,
-            bigBedLocation: file
-          };
-
-          if (regexGuess.test(fileName) && !adapterHint) {
-            return obj;
-          } else if (adapterHint === adapterName) {
-            return obj;
-          }
-
-          return adapterGuesser(file, index, adapterHint);
-        };
-      });
-      pluginManager.addAdapterType(function () {
-        return new _AdapterType.default({
-          name: 'BedTabixAdapter',
-          configSchema: _BedTabixAdapter.configSchema,
-          getAdapterClass: function getAdapterClass() {
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('./BedTabixAdapter/BedTabixAdapter'));
-            }).then(function (r) {
-              return r.default;
+        pluginManager.addAdapterType(function () {
+            return new AdapterType_1.default({
+                name: 'BedAdapter',
+                configSchema: BedAdapter_1.configSchema,
+                getAdapterClass: function () {
+                    return Promise.resolve().then(function () { return __importStar(require('./BedAdapter/BedAdapter')); }).then(function (r) { return r.default; });
+                },
             });
-          }
         });
-      });
-      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
-        return function (file, index, adapterHint) {
-          var regexGuess = /\.bed\.b?gz$/i;
-          var adapterName = 'BedTabixAdapter';
-          var fileName = (0, _tracks.getFileName)(file);
-          var indexName = index && (0, _tracks.getFileName)(index);
-
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              bedGzLocation: file,
-              index: {
-                location: index || (0, _tracks.makeIndex)(file, '.tbi'),
-                indexType: (0, _tracks.makeIndexType)(indexName, 'CSI', 'TBI')
-              }
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+            return function (file, index, adapterHint) {
+                var regexGuess = /\.bed\.b?gz$/i;
+                var adapterName = 'BedTabixAdapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                var indexName = index && (0, tracks_1.getFileName)(index);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        bedGzLocation: file,
+                        index: {
+                            location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
+                            indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
+                        },
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
             };
-          }
-
-          return adapterGuesser(file, index, adapterHint);
-        };
-      });
-    }
-  }]);
-  return BedPlugin;
-}(_Plugin2.default);
-
-exports.default = BedPlugin;
+        });
+        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+            return function (file, index, adapterHint) {
+                var regexGuess = /\.bed$/i;
+                var adapterName = 'BedAdapter';
+                var fileName = (0, tracks_1.getFileName)(file);
+                if (regexGuess.test(fileName) || adapterHint === adapterName) {
+                    return {
+                        type: adapterName,
+                        bedLocation: file,
+                    };
+                }
+                return adapterGuesser(file, index, adapterHint);
+            };
+        });
+    };
+    return BedPlugin;
+}(Plugin_1.default));
+exports.default = BedPlugin;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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

@@ -1,2 +1,4 @@
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature';
+import { SimpleFeature, Feature } from '@jbrowse/core/util';
+import BED from '@gmod/bed';
 export declare function ucscProcessedTranscript(feature: Feature): Feature | SimpleFeature;
+export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: typeof BED, uniqueId: string, names?: string[]): Feature | SimpleFeature;

package/dist/util.js

@@ -1,124 +1,164 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.ucscProcessedTranscript = ucscProcessedTranscript;
-
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.featureData = exports.ucscProcessedTranscript = void 0;
+var util_1 = require("@jbrowse/core/util");
 function ucscProcessedTranscript(feature) {
-  var children = feature.children(); // split the blocks into UTR, CDS, and exons
-
-  var thickStart = feature.get('thickStart');
-  var thickEnd = feature.get('thickEnd');
-
-  if (!thickStart && !thickEnd) {
-    return feature;
-  }
-
-  var blocks = children ? children.filter(function (child) {
-    return child.get('type') === 'block';
-  }).sort(function (a, b) {
-    return a.get('start') - b.get('start');
-  }) : []; // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-  var newChildren = [];
-  blocks.forEach(function (block) {
-    var start = block.get('start');
-    var end = block.get('end');
-
-    if (thickStart >= end) {
-      // left-side UTR
-      var prime = feature.get('strand') > 0 ? 'five' : 'three';
-      newChildren.push({
-        type: "".concat(prime, "_prime_UTR"),
-        start: start,
-        end: end
-      });
-    } else if (thickStart > start && thickStart < end && thickEnd >= end) {
-      // UTR | CDS
-      var _prime = feature.get('strand') > 0 ? 'five' : 'three';
-
-      newChildren.push({
-        type: "".concat(_prime, "_prime_UTR"),
-        start: start,
-        end: thickStart
-      }, {
-        type: 'CDS',
-        start: thickStart,
-        end: end
-      });
-    } else if (thickStart <= start && thickEnd >= end) {
-      // CDS
-      newChildren.push({
-        type: 'CDS',
-        start: start,
-        end: end
-      });
-    } else if (thickStart > start && thickStart < end && thickEnd < end) {
-      // UTR | CDS | UTR
-      var leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
-      var rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
-      newChildren.push({
-        type: "".concat(leftPrime, "_prime_UTR"),
-        start: start,
-        end: thickStart
-      }, {
-        type: "CDS",
-        start: thickStart,
-        end: thickEnd
-      }, {
-        type: "".concat(rightPrime, "_prime_UTR"),
-        start: thickEnd,
-        end: end
-      });
-    } else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-      // CDS | UTR
-      var _prime2 = feature.get('strand') > 0 ? 'three' : 'five';
-
-      newChildren.push({
-        type: "CDS",
-        start: start,
-        end: thickEnd
-      }, {
-        type: "".concat(_prime2, "_prime_UTR"),
-        start: thickEnd,
-        end: end
-      });
-    } else if (thickEnd <= start) {
-      // right-side UTR
-      var _prime3 = feature.get('strand') > 0 ? 'three' : 'five';
-
-      newChildren.push({
-        type: "".concat(_prime3, "_prime_UTR"),
-        start: start,
-        end: end
-      });
+    var children = feature.children();
+    // split the blocks into UTR, CDS, and exons
+    var thickStart = feature.get('thickStart');
+    var thickEnd = feature.get('thickEnd');
+    if (!thickStart && !thickEnd) {
+        return feature;
+    }
+    var blocks = children
+        ? children
+            .filter(function (child) { return child.get('type') === 'block'; })
+            .sort(function (a, b) { return a.get('start') - b.get('start'); })
+        : [];
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    var newChildren = [];
+    blocks.forEach(function (block) {
+        var start = block.get('start');
+        var end = block.get('end');
+        if (thickStart >= end) {
+            // left-side UTR
+            var prime = feature.get('strand') > 0 ? 'five' : 'three';
+            newChildren.push({
+                type: "".concat(prime, "_prime_UTR"),
+                start: start,
+                end: end,
+            });
+        }
+        else if (thickStart > start && thickStart < end && thickEnd >= end) {
+            // UTR | CDS
+            var prime = feature.get('strand') > 0 ? 'five' : 'three';
+            newChildren.push({
+                type: "".concat(prime, "_prime_UTR"),
+                start: start,
+                end: thickStart,
+            }, {
+                type: 'CDS',
+                start: thickStart,
+                end: end,
+            });
+        }
+        else if (thickStart <= start && thickEnd >= end) {
+            // CDS
+            newChildren.push({
+                type: 'CDS',
+                start: start,
+                end: end,
+            });
+        }
+        else if (thickStart > start && thickStart < end && thickEnd < end) {
+            // UTR | CDS | UTR
+            var leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
+            var rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
+            newChildren.push({
+                type: "".concat(leftPrime, "_prime_UTR"),
+                start: start,
+                end: thickStart,
+            }, {
+                type: "CDS",
+                start: thickStart,
+                end: thickEnd,
+            }, {
+                type: "".concat(rightPrime, "_prime_UTR"),
+                start: thickEnd,
+                end: end,
+            });
+        }
+        else if (thickStart <= start && thickEnd > start && thickEnd < end) {
+            // CDS | UTR
+            var prime = feature.get('strand') > 0 ? 'three' : 'five';
+            newChildren.push({
+                type: "CDS",
+                start: start,
+                end: thickEnd,
+            }, {
+                type: "".concat(prime, "_prime_UTR"),
+                start: thickEnd,
+                end: end,
+            });
+        }
+        else if (thickEnd <= start) {
+            // right-side UTR
+            var prime = feature.get('strand') > 0 ? 'three' : 'five';
+            newChildren.push({
+                type: "".concat(prime, "_prime_UTR"),
+                start: start,
+                end: end,
+            });
+        }
+    });
+    var newData = Object.fromEntries(feature.tags().map(function (tag) { return [tag, feature.get(tag)]; }));
+    newData.subfeatures = newChildren;
+    newData.type = 'mRNA';
+    newData.uniqueId = feature.id();
+    delete newData.chromStarts;
+    delete newData.chromStart;
+    delete newData.chromEnd;
+    delete newData.chrom;
+    delete newData.blockStarts;
+    delete newData.blockSizes;
+    delete newData.blockCount;
+    delete newData.thickStart;
+    delete newData.thickEnd;
+    var newFeature = new util_1.SimpleFeature({
+        data: newData,
+        id: feature.id(),
+    });
+    return newFeature;
+}
+exports.ucscProcessedTranscript = ucscProcessedTranscript;
+function defaultParser(fields, line) {
+    return Object.fromEntries(line.split('\t').map(function (f, i) { return [fields[i], f]; }));
+}
+function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names) {
+    var l = line.split('\t');
+    var refName = l[colRef];
+    var start = +l[colStart];
+    var colSame = colStart === colEnd ? 1 : 0;
+    var end = +l[colEnd] + colSame;
+    var data = names
+        ? defaultParser(names, line)
+        : parser.parseLine(line, { uniqueId: uniqueId });
+    var blockCount = data.blockCount, blockSizes = data.blockSizes, blockStarts = data.blockStarts, chromStarts = data.chromStarts;
+    if (blockCount) {
+        var starts = chromStarts || blockStarts || [];
+        var sizes = blockSizes;
+        var blocksOffset = start;
+        data.subfeatures = [];
+        for (var b = 0; b < blockCount; b += 1) {
+            var bmin = (starts[b] || 0) + blocksOffset;
+            var bmax = bmin + (sizes[b] || 0);
+            data.subfeatures.push({
+                uniqueId: "".concat(uniqueId, "-").concat(b),
+                start: bmin,
+                end: bmax,
+                type: 'block',
+            });
+        }
+    }
+    if (scoreColumn) {
+        data.score = +data[scoreColumn];
     }
-  }); // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-  var newData = {};
-  feature.tags().forEach(function (tag) {
-    newData[tag] = feature.get(tag);
-  });
-  newData.subfeatures = newChildren;
-  newData.type = 'mRNA';
-  newData.uniqueId = feature.id();
-  delete newData.chromStarts;
-  delete newData.chromStart;
-  delete newData.chromEnd;
-  delete newData.chrom;
-  delete newData.blockStarts;
-  delete newData.blockSizes;
-  delete newData.blockCount;
-  delete newData.thickStart;
-  delete newData.thickEnd;
-  var newFeature = new _simpleFeature.default({
-    data: newData,
-    id: feature.id()
-  });
-  return newFeature;
-}
+    delete data.chrom;
+    delete data.chromStart;
+    delete data.chromEnd;
+    var f = new util_1.SimpleFeature(__assign(__assign({}, data), { start: start, end: end, refName: refName, uniqueId: uniqueId }));
+    return f.get('thickStart') ? ucscProcessedTranscript(f) : f;
+}
+exports.featureData = featureData;
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

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package/esm/BedAdapter/BedAdapter.d.ts

@@ -0,0 +1,29 @@
+import BED from '@gmod/bed';
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region, Feature } from '@jbrowse/core/util';
+import IntervalTree from '@flatten-js/interval-tree';
+export default class BedAdapter extends BaseFeatureDataAdapter {
+    protected bedFeatures?: Promise<{
+        header: string;
+        features: Record<string, string[]>;
+        parser: typeof BED;
+        columnNames: string[];
+        scoreColumn: string;
+        colRef: number;
+        colStart: number;
+        colEnd: number;
+    }>;
+    protected intervalTrees: {
+        [key: string]: Promise<IntervalTree | undefined> | undefined;
+    };
+    static capabilities: string[];
+    private loadDataP;
+    private loadData;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(opts?: BaseOptions): Promise<string>;
+    getNames(): Promise<string[] | undefined>;
+    private loadFeatureIntervalTreeHelper;
+    private loadFeatureIntervalTree;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}