@jbrowse/plugin-data-management 1.7.11 → 2.0.0

package/dist/ucsc-trackhub/ucscTrackHub.js

@@ -1,503 +1,470 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.fetchGenomesFile = fetchGenomesFile;
-exports.fetchHubFile = fetchHubFile;
-exports.fetchTrackDbFile = fetchTrackDbFile;
-exports.generateTracks = generateTracks;
-Object.defineProperty(exports, "ucscAssemblies", {
-  enumerable: true,
-  get: function get() {
-    return _ucscAssemblies.default;
-  }
+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;
 });
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _util = require("@jbrowse/core/util");
-
-var _io = require("@jbrowse/core/util/io");
-
-var _tracks = require("@jbrowse/core/util/tracks");
-
-var _ucscAssemblies = _interopRequireDefault(require("./ucscAssemblies"));
-
-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 fetchHubFile(_x) {
-  return _fetchHubFile.apply(this, arguments);
-}
-
-function _fetchHubFile() {
-  _fetchHubFile = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(hubFileLocation) {
-    var hubFileText, _yield$import, HubFile;
-
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            _context.prev = 0;
-            _context.next = 3;
-            return (0, _io.openLocation)(hubFileLocation).readFile('utf8');
-
-          case 3:
-            hubFileText = _context.sent;
-            _context.next = 6;
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('@gmod/ucsc-hub'));
-            });
-
-          case 6:
-            _yield$import = _context.sent;
-            HubFile = _yield$import.HubFile;
-            return _context.abrupt("return", new HubFile(hubFileText));
-
-          case 11:
-            _context.prev = 11;
-            _context.t0 = _context["catch"](0);
-            throw new Error("Not a valid hub.txt file, got error: '".concat(_context.t0, "'"));
-
-          case 14:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee, null, [[0, 11]]);
-  }));
-  return _fetchHubFile.apply(this, arguments);
-}
-
-function fetchGenomesFile(_x2) {
-  return _fetchGenomesFile.apply(this, arguments);
-}
-
-function _fetchGenomesFile() {
-  _fetchGenomesFile = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(genomesFileLocation) {
-    var genomesFileText, _yield$import2, GenomesFile;
-
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            _context2.next = 2;
-            return (0, _io.openLocation)(genomesFileLocation).readFile('utf8');
-
-          case 2:
-            genomesFileText = _context2.sent;
-            _context2.next = 5;
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('@gmod/ucsc-hub'));
-            });
-
-          case 5:
-            _yield$import2 = _context2.sent;
-            GenomesFile = _yield$import2.GenomesFile;
-            return _context2.abrupt("return", new GenomesFile(genomesFileText));
-
-          case 8:
-          case "end":
-            return _context2.stop();
+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 __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 __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
         }
-      }
-    }, _callee2);
-  }));
-  return _fetchGenomesFile.apply(this, arguments);
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.generateTracks = exports.fetchTrackDbFile = exports.fetchGenomesFile = exports.fetchHubFile = exports.ucscAssemblies = void 0;
+var util_1 = require("@jbrowse/core/util");
+var io_1 = require("@jbrowse/core/util/io");
+var tracks_1 = require("@jbrowse/core/util/tracks");
+var ucscAssemblies_1 = __importDefault(require("./ucscAssemblies"));
+exports.ucscAssemblies = ucscAssemblies_1.default;
+function fetchHubFile(hubFileLocation) {
+    return __awaiter(this, void 0, void 0, function () {
+        var hubFileText, HubFile, error_1;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    _a.trys.push([0, 3, , 4]);
+                    return [4 /*yield*/, (0, io_1.openLocation)(hubFileLocation).readFile('utf8')];
+                case 1:
+                    hubFileText = _a.sent();
+                    return [4 /*yield*/, Promise.resolve().then(function () { return __importStar(require('@gmod/ucsc-hub')); })];
+                case 2:
+                    HubFile = (_a.sent()).HubFile;
+                    return [2 /*return*/, new HubFile(hubFileText)];
+                case 3:
+                    error_1 = _a.sent();
+                    throw new Error("Not a valid hub.txt file, got error: '".concat(error_1, "'"));
+                case 4: return [2 /*return*/];
+            }
+        });
+    });
 }
-
-function fetchTrackDbFile(_x3) {
-  return _fetchTrackDbFile.apply(this, arguments);
+exports.fetchHubFile = fetchHubFile;
+function fetchGenomesFile(genomesFileLocation) {
+    return __awaiter(this, void 0, void 0, function () {
+        var genomesFileText, GenomesFile;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, (0, io_1.openLocation)(genomesFileLocation).readFile('utf8')];
+                case 1:
+                    genomesFileText = _a.sent();
+                    return [4 /*yield*/, Promise.resolve().then(function () { return __importStar(require('@gmod/ucsc-hub')); })];
+                case 2:
+                    GenomesFile = (_a.sent()).GenomesFile;
+                    return [2 /*return*/, new GenomesFile(genomesFileText)];
+            }
+        });
+    });
 }
-
-function _fetchTrackDbFile() {
-  _fetchTrackDbFile = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(trackDbFileLocation) {
-    var text, _yield$import3, TrackDbFile;
-
-    return _regenerator.default.wrap(function _callee3$(_context3) {
-      while (1) {
-        switch (_context3.prev = _context3.next) {
-          case 0:
-            _context3.next = 2;
-            return (0, _io.openLocation)(trackDbFileLocation).readFile('utf8');
-
-          case 2:
-            text = _context3.sent;
-            _context3.next = 5;
-            return Promise.resolve().then(function () {
-              return _interopRequireWildcard(require('@gmod/ucsc-hub'));
-            });
-
-          case 5:
-            _yield$import3 = _context3.sent;
-            TrackDbFile = _yield$import3.TrackDbFile;
-            return _context3.abrupt("return", new TrackDbFile(text));
-
-          case 8:
-          case "end":
-            return _context3.stop();
-        }
-      }
-    }, _callee3);
-  }));
-  return _fetchTrackDbFile.apply(this, arguments);
+exports.fetchGenomesFile = fetchGenomesFile;
+function fetchTrackDbFile(trackDbFileLocation) {
+    return __awaiter(this, void 0, void 0, function () {
+        var text, TrackDbFile;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, (0, io_1.openLocation)(trackDbFileLocation).readFile('utf8')];
+                case 1:
+                    text = _a.sent();
+                    return [4 /*yield*/, Promise.resolve().then(function () { return __importStar(require('@gmod/ucsc-hub')); })];
+                case 2:
+                    TrackDbFile = (_a.sent()).TrackDbFile;
+                    return [2 /*return*/, new TrackDbFile(text)];
+            }
+        });
+    });
 }
-
+exports.fetchTrackDbFile = fetchTrackDbFile;
 function generateTracks(trackDb, trackDbFileLocation, assemblyName, sequenceAdapter) {
-  var tracks = [];
-  trackDb.forEach(function (track, trackName) {
-    var trackKeys = Array.from(track.keys());
-    var parentTrackKeys = ['superTrack', 'compositeTrack', 'container', 'view'];
-
-    if (trackKeys.some(function (key) {
-      return parentTrackKeys.includes(key);
-    })) {
-      return;
-    }
-
-    var parentTracks = [];
-    var currentTrackName = trackName;
-
-    do {
-      currentTrackName = trackDb.get(currentTrackName).get('parent');
-
-      if (currentTrackName) {
-        ;
-
-        var _currentTrackName$spl = currentTrackName.split(' ');
-
-        var _currentTrackName$spl2 = (0, _slicedToArray2.default)(_currentTrackName$spl, 1);
-
-        currentTrackName = _currentTrackName$spl2[0];
-        parentTracks.push(trackDb.get(currentTrackName));
-      }
-    } while (currentTrackName);
-
-    parentTracks.reverse();
-    var categories = parentTracks.map(function (parentTrack) {
-      return parentTrack.get('shortLabel');
+    var tracks = [];
+    trackDb.forEach(function (track, trackName) {
+        var _a;
+        var trackKeys = Array.from(track.keys());
+        var parentTrackKeys = [
+            'superTrack',
+            'compositeTrack',
+            'container',
+            'view',
+        ];
+        if (trackKeys.some(function (key) { return parentTrackKeys.includes(key); })) {
+            return;
+        }
+        var parentTracks = [];
+        var currentTrackName = trackName;
+        do {
+            currentTrackName = trackDb.get(currentTrackName).get('parent');
+            if (currentTrackName) {
+                ;
+                _a = __read(currentTrackName.split(' '), 1), currentTrackName = _a[0];
+                parentTracks.push(trackDb.get(currentTrackName));
+            }
+        } while (currentTrackName);
+        parentTracks.reverse();
+        var categories = parentTracks.map(function (parentTrack) {
+            return parentTrack.get('shortLabel');
+        });
+        var res = makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter);
+        res.trackId = "ucsc-trackhub-".concat((0, util_1.objectHash)(res));
+        res.assemblyNames = [assemblyName];
+        tracks.push(res);
     });
-    var res = makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter);
-    res.trackId = "ucsc-trackhub-".concat((0, _util.objectHash)(res));
-    res.assemblyNames = [assemblyName];
-    tracks.push(res);
-  });
-  return tracks;
+    return tracks;
 }
-
+exports.generateTracks = generateTracks;
 function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter) {
-  var trackType = track.get('type');
-
-  if (!trackType) {
-    trackType = trackDb.get(track.get('parent')).get('type');
-  }
-
-  var baseTrackType = trackType.split(' ')[0];
-
-  if (baseTrackType === 'bam' && track.get('bigDataUrl').toLowerCase().endsWith('cram')) {
-    baseTrackType = 'cram';
-  }
-
-  var bigDataLocation;
-
-  if (trackDbFileLocation.uri) {
-    bigDataLocation = {
-      uri: new URL(track.get('bigDataUrl'), trackDbFileLocation.uri).href,
-      locationType: 'UriLocation'
-    };
-  } else {
-    bigDataLocation = {
-      localPath: track.get('bigDataUrl'),
-      locationType: 'LocalPathLocation'
-    };
-  }
-
-  var bigDataIndexLocation;
-
-  switch (baseTrackType) {
-    case 'bam':
-      if (trackDbFileLocation.uri) {
-        bigDataIndexLocation = track.get('bigDataIndex') ? {
-          uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri).href,
-          locationType: 'UriLocation'
-        } : {
-          uri: new URL("".concat(track.get('bigDataUrl'), ".bai"), trackDbFileLocation.uri).href,
-          locationType: 'UriLocation'
-        };
-      } else {
-        bigDataIndexLocation = track.get('bigDataIndex') ? {
-          localPath: track.get('bigDataIndex'),
-          locationType: 'LocalPathLocation'
-        } : {
-          localPath: "".concat(track.get('bigDataUrl'), ".bai"),
-          locationType: 'LocalPathLocation'
-        };
-      }
-
-      return {
-        type: 'AlignmentsTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BamAdapter',
-          bamLocation: bigDataLocation,
-          index: {
-            location: bigDataIndexLocation
-          }
-        }
-      };
-
-    case 'bed':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'bed5FloatScore':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'bedGraph':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'bedRnaElements':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'bigBarChart':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer'
-        }
-      };
-
-    case 'bigBed':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation
-        }
-      };
-
-    case 'bigGenePred':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation
-        }
-      };
-
-    case 'bigChain':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer'
-        }
-      };
-
-    case 'bigInteract':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer'
-        }
-      };
-
-    case 'bigMaf':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer'
-        }
-      };
-
-    case 'bigPsl':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer'
-        }
-      };
-
-    case 'bigWig':
-      return {
-        type: 'QuantitativeTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigWigAdapter',
-          bigWigLocation: bigDataLocation
-        }
-      };
-
-    case 'broadPeak':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'coloredExon':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'cram':
-      if (trackDbFileLocation.uri) {
-        bigDataIndexLocation = track.get('bigDataIndex') ? {
-          uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri).href,
-          locationType: 'UriLocation'
-        } : {
-          uri: new URL("".concat(track.get('bigDataUrl'), ".crai"), trackDbFileLocation.uri).href,
-          locationType: 'UriLocation'
-        };
-      } else {
-        bigDataIndexLocation = track.get('bigDataIndex') ? {
-          localPath: track.get('bigDataIndex'),
-          locationType: 'LocalPathLocation'
-        } : {
-          localPath: "".concat(track.get('bigDataUrl'), ".crai"),
-          locationType: 'LocalPathLocation'
-        };
-      }
-
-      return {
-        type: 'AlignmentsTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'CramAdapter',
-          cramLocation: bigDataLocation,
-          craiLocation: bigDataIndexLocation,
-          sequenceAdapter: sequenceAdapter
-        }
-      };
-
-    case 'gvf':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'ld2':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'narrowPeak':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'bigNarrowPeak':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation
-        }
-      };
-
-    case 'peptideMapping':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'vcfTabix':
-      if (trackDbFileLocation.uri) {
-        bigDataIndexLocation = track.get('bigDataIndex') ? {
-          uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri).href,
-          locationType: 'UriLocation'
-        } : {
-          uri: new URL("".concat(track.get('bigDataUrl'), ".tbi"), trackDbFileLocation.uri).href,
-          locationType: 'UriLocation'
+    var trackType = track.get('type');
+    if (!trackType) {
+        trackType = trackDb.get(track.get('parent')).get('type');
+    }
+    var baseTrackType = trackType.split(' ')[0];
+    if (baseTrackType === 'bam' &&
+        track.get('bigDataUrl').toLowerCase().endsWith('cram')) {
+        baseTrackType = 'cram';
+    }
+    var bigDataLocation;
+    if (trackDbFileLocation.uri) {
+        bigDataLocation = {
+            uri: new URL(track.get('bigDataUrl'), trackDbFileLocation.uri).href,
+            locationType: 'UriLocation',
         };
-      } else {
-        bigDataIndexLocation = track.get('bigDataIndex') ? {
-          localPath: track.get('bigDataIndex'),
-          locationType: 'LocalPathLocation'
-        } : {
-          localPath: "".concat(track.get('bigDataUrl'), ".tbi"),
-          locationType: 'LocalPathLocation'
+    }
+    else {
+        bigDataLocation = {
+            localPath: track.get('bigDataUrl'),
+            locationType: 'LocalPathLocation',
         };
-      }
-
-      return {
-        type: 'VariantTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'VcfTabixAdapter',
-          vcfGzLocation: bigDataLocation,
-          index: {
-            location: bigDataIndexLocation
-          }
-        }
-      };
-
-    case 'wig':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'wigMaf':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    case 'hic':
-      return {
-        type: 'HicTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'HicAdapter',
-          hicLocation: bigDataLocation
-        }
-      };
-
-    case 'halSnake':
-      return (0, _tracks.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-
-    default:
-      return (0, _tracks.generateUnknownTrackConf)(track.get('shortLabel'), baseTrackType, categories);
-  }
-}
+    }
+    var bigDataIndexLocation;
+    switch (baseTrackType) {
+        case 'bam':
+            if (trackDbFileLocation.uri) {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
+                            .href,
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        uri: new URL("".concat(track.get('bigDataUrl'), ".bai"), trackDbFileLocation.uri).href,
+                        locationType: 'UriLocation',
+                    };
+            }
+            else {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        localPath: track.get('bigDataIndex'),
+                        locationType: 'LocalPathLocation',
+                    }
+                    : {
+                        localPath: "".concat(track.get('bigDataUrl'), ".bai"),
+                        locationType: 'LocalPathLocation',
+                    };
+            }
+            return {
+                type: 'AlignmentsTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BamAdapter',
+                    bamLocation: bigDataLocation,
+                    index: {
+                        location: bigDataIndexLocation,
+                    },
+                },
+            };
+        case 'bed':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'bed5FloatScore':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'bedGraph':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'bedRnaElements':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'bigBarChart':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+                renderer: {
+                    type: 'SvgFeatureRenderer',
+                },
+            };
+        case 'bigBed':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+            };
+        case 'bigGenePred':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+            };
+        case 'bigChain':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+                renderer: {
+                    type: 'SvgFeatureRenderer',
+                },
+            };
+        case 'bigInteract':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+                renderer: {
+                    type: 'SvgFeatureRenderer',
+                },
+            };
+        case 'bigMaf':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+                renderer: {
+                    type: 'SvgFeatureRenderer',
+                },
+            };
+        case 'bigPsl':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+                renderer: {
+                    type: 'SvgFeatureRenderer',
+                },
+            };
+        case 'bigWig':
+            return {
+                type: 'QuantitativeTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigWigAdapter',
+                    bigWigLocation: bigDataLocation,
+                },
+            };
+        case 'broadPeak':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'coloredExon':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'cram':
+            if (trackDbFileLocation.uri) {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
+                            .href,
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        uri: new URL("".concat(track.get('bigDataUrl'), ".crai"), trackDbFileLocation.uri).href,
+                        locationType: 'UriLocation',
+                    };
+            }
+            else {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        localPath: track.get('bigDataIndex'),
+                        locationType: 'LocalPathLocation',
+                    }
+                    : {
+                        localPath: "".concat(track.get('bigDataUrl'), ".crai"),
+                        locationType: 'LocalPathLocation',
+                    };
+            }
+            return {
+                type: 'AlignmentsTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'CramAdapter',
+                    cramLocation: bigDataLocation,
+                    craiLocation: bigDataIndexLocation,
+                    sequenceAdapter: sequenceAdapter,
+                },
+            };
+        case 'gvf':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'ld2':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'narrowPeak':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'bigNarrowPeak':
+            return {
+                type: 'FeatureTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: bigDataLocation,
+                },
+            };
+        case 'peptideMapping':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'vcfTabix':
+            if (trackDbFileLocation.uri) {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
+                            .href,
+                        locationType: 'UriLocation',
+                    }
+                    : {
+                        uri: new URL("".concat(track.get('bigDataUrl'), ".tbi"), trackDbFileLocation.uri).href,
+                        locationType: 'UriLocation',
+                    };
+            }
+            else {
+                bigDataIndexLocation = track.get('bigDataIndex')
+                    ? {
+                        localPath: track.get('bigDataIndex'),
+                        locationType: 'LocalPathLocation',
+                    }
+                    : {
+                        localPath: "".concat(track.get('bigDataUrl'), ".tbi"),
+                        locationType: 'LocalPathLocation',
+                    };
+            }
+            return {
+                type: 'VariantTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'VcfTabixAdapter',
+                    vcfGzLocation: bigDataLocation,
+                    index: {
+                        location: bigDataIndexLocation,
+                    },
+                },
+            };
+        case 'wig':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'wigMaf':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        case 'hic':
+            return {
+                type: 'HicTrack',
+                name: track.get('shortLabel'),
+                description: track.get('longLabel'),
+                category: categories,
+                adapter: {
+                    type: 'HicAdapter',
+                    hicLocation: bigDataLocation,
+                },
+            };
+        case 'halSnake':
+            return (0, tracks_1.generateUnsupportedTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+        default:
+            return (0, tracks_1.generateUnknownTrackConf)(track.get('shortLabel'), baseTrackType, categories);
+    }
+}
+//# sourceMappingURL=ucscTrackHub.js.map