@jbrowse/plugin-legacy-jbrowse 1.7.9 → 2.0.0

package/dist/JBrowse1Connection/jb1ToJb2.js

@@ -1,574 +1,433 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.convertTrackConfig = convertTrackConfig;
-exports.createRefSeqsAdapter = createRefSeqsAdapter;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _io = require("@jbrowse/core/util/io");
-
-var _util = require("@jbrowse/core/util");
-
-var _tracks = require("@jbrowse/core/util/tracks");
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
-function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
-  var jb2TrackConfig = {
-    trackId: (0, _util.objectHash)(jb1TrackConfig),
-    name: jb1TrackConfig.key || jb1TrackConfig.label
-  };
-  var description = jb1TrackConfig.metadata && (jb1TrackConfig.metadata.description || jb1TrackConfig.metadata.Description);
-
-  if (description) {
-    jb2TrackConfig.description = description;
-  }
-
-  var category = jb1TrackConfig.category || jb1TrackConfig.metadata && jb1TrackConfig.metadata.category;
-  jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
-  var storeClass = jb1TrackConfig.storeClass;
-
-  if (!jb1TrackConfig.urlTemplate) {
-    if (!(storeClass && storeClass.endsWith('FromConfig'))) {
-      var trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
-      console.warn("Could not import JBrowse1 track \"".concat(trackIdentifier, "\" because it does not have a \"urlTemplate\" or is not a \"FromConfig\" track"));
-      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
-    }
-
-    return generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig);
-  }
-
-  var resolveUrlTemplate = function resolveUrlTemplate(urlTemplate) {
-    return new URL(urlTemplate, "".concat(dataRoot, "/")).href.replace(/%7B/gi, '{').replace(/%7D/gi, '}');
-  };
-
-  var urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate);
-
-  if (storeClass) {
-    if (storeClass === 'JBrowse/Store/SeqFeature/BAM') {
-      var adapter = {
-        type: 'BamAdapter',
-        bamLocation: {
-          uri: urlTemplate,
-          locationType: 'UriLocation'
+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];
         }
-      };
-
-      if (jb1TrackConfig.baiUrlTemplate) {
-        adapter.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate),
-            locationType: 'UriLocation'
-          }
-        };
-      } else if (jb1TrackConfig.csiUrlTemplate) {
-        adapter.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-            locationType: 'UriLocation'
-          },
-          indexType: 'CSI'
-        };
-      } else {
-        adapter.index = {
-          location: {
-            uri: "".concat(urlTemplate, ".bai"),
-            locationType: 'UriLocation'
-          }
-        };
-      }
-
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'AlignmentsTrack',
-        adapter: adapter
-      });
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+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 };
     }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/CRAM') {
-      var _adapter = {
-        type: 'CramAdapter',
-        cramLocation: {
-          uri: urlTemplate,
-          locationType: 'UriLocation'
-        },
-        sequenceAdapter: sequenceAdapter
-      };
-
-      if (jb1TrackConfig.craiUrlTemplate) {
-        _adapter.craiLocation = {
-          uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
-          locationType: 'UriLocation'
-        };
-      } else {
-        _adapter.craiLocation = {
-          uri: "".concat(urlTemplate, ".crai"),
-          locationType: 'UriLocation'
-        };
-      }
-
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'AlignmentsTrack',
-        adapter: _adapter
-      });
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createRefSeqsAdapter = exports.convertTrackConfig = void 0;
+var io_1 = require("@jbrowse/core/util/io");
+var util_1 = require("@jbrowse/core/util");
+var tracks_1 = require("@jbrowse/core/util/tracks");
+function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
+    var jb2TrackConfig = {
+        trackId: (0, util_1.objectHash)(jb1TrackConfig),
+        name: jb1TrackConfig.key || jb1TrackConfig.label,
+    };
+    var description = jb1TrackConfig.metadata &&
+        (jb1TrackConfig.metadata.description || jb1TrackConfig.metadata.Description);
+    if (description) {
+        jb2TrackConfig.description = description;
     }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/NCList') {
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'FeatureTrack',
-        adapter: {
-          type: 'NCListAdapter',
-          rootUrlTemplate: {
-            uri: urlTemplate,
-            locationType: 'UriLocation'
-          }
+    var category = jb1TrackConfig.category ||
+        (jb1TrackConfig.metadata && jb1TrackConfig.metadata.category);
+    jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : [];
+    var storeClass = jb1TrackConfig.storeClass;
+    if (!jb1TrackConfig.urlTemplate) {
+        if (!(storeClass && storeClass.endsWith('FromConfig'))) {
+            var trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label;
+            console.warn("Could not import JBrowse1 track \"".concat(trackIdentifier, "\" because it does not have a \"urlTemplate\" or is not a \"FromConfig\" track"));
+            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, trackIdentifier, jb2TrackConfig.category);
         }
-      });
+        return generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig);
     }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' || storeClass === 'JBrowse/Store/BigWig') {
-      if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
-        jb2TrackConfig.defaultRendering = 'xyplot';
-      } else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
-        jb2TrackConfig.defaultRendering = 'density';
-      }
-
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'QuantitativeTrack',
-        adapter: {
-          type: 'BigWigAdapter',
-          bigWigLocation: {
-            uri: urlTemplate,
-            locationType: 'UriLocation'
-          }
+    var resolveUrlTemplate = function (urlTemplate) {
+        return new URL(urlTemplate, "".concat(dataRoot, "/")).href
+            .replace(/%7B/gi, '{')
+            .replace(/%7D/gi, '}');
+    };
+    var urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate);
+    if (storeClass) {
+        if (storeClass === 'JBrowse/Store/SeqFeature/BAM') {
+            var adapter = {
+                type: 'BamAdapter',
+                bamLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.baiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                };
+            }
+            else if (jb1TrackConfig.csiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                    indexType: 'CSI',
+                };
+            }
+            else {
+                adapter.index = {
+                    location: { uri: "".concat(urlTemplate, ".bai"), locationType: 'UriLocation' },
+                };
+            }
+            return __assign(__assign({}, jb2TrackConfig), { type: 'AlignmentsTrack', adapter: adapter });
         }
-      });
-    }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/VCFTabix') {
-      var _adapter2 = {
-        type: 'VcfTabixAdapter',
-        vcfGzLocation: {
-          uri: urlTemplate,
-          locationType: 'UriLocation'
+        if (storeClass === 'JBrowse/Store/SeqFeature/CRAM') {
+            var adapter = {
+                type: 'CramAdapter',
+                cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                sequenceAdapter: sequenceAdapter,
+            };
+            if (jb1TrackConfig.craiUrlTemplate) {
+                adapter.craiLocation = {
+                    uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
+                    locationType: 'UriLocation',
+                };
+            }
+            else {
+                adapter.craiLocation = {
+                    uri: "".concat(urlTemplate, ".crai"),
+                    locationType: 'UriLocation',
+                };
+            }
+            return __assign(__assign({}, jb2TrackConfig), { type: 'AlignmentsTrack', adapter: adapter });
         }
-      };
-
-      if (jb1TrackConfig.tbiUrlTemplate) {
-        _adapter2.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-            locationType: 'UriLocation'
-          }
-        };
-      } else if (jb1TrackConfig.csiUrlTemplate) {
-        _adapter2.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-            locationType: 'UriLocation'
-          },
-          indexType: 'CSI'
-        };
-      } else {
-        _adapter2.index = {
-          location: {
-            uri: "".concat(urlTemplate, ".tbi"),
-            locationType: 'UriLocation'
-          }
-        };
-      }
-
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'VariantTrack',
-        adapter: _adapter2
-      });
-    }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/VCFTribble') {
-      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "VCFTribble (".concat(urlTemplate, ")"), jb2TrackConfig.category);
-    }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'FeatureTrack',
-        adapter: {
-          type: 'Gff3Adapter',
-          gffLocation: {
-            uri: urlTemplate,
-            locationType: 'UriLocation'
-          }
+        if (storeClass === 'JBrowse/Store/SeqFeature/NCList') {
+            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: {
+                    type: 'NCListAdapter',
+                    rootUrlTemplate: { uri: urlTemplate, locationType: 'UriLocation' },
+                } });
         }
-      });
-    }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'FeatureTrack',
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: {
-            uri: urlTemplate,
-            locationType: 'UriLocation'
-          }
+        if (storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
+            storeClass === 'JBrowse/Store/BigWig') {
+            if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+                jb2TrackConfig.defaultRendering = 'xyplot';
+            }
+            else if (jb1TrackConfig.type &&
+                jb1TrackConfig.type.endsWith('Density')) {
+                jb2TrackConfig.defaultRendering = 'density';
+            }
+            return __assign(__assign({}, jb2TrackConfig), { type: 'QuantitativeTrack', adapter: {
+                    type: 'BigWigAdapter',
+                    bigWigLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                } });
         }
-      });
-    }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/GFF3Tabix') {
-      var _adapter3 = {
-        type: 'Gff3TabixAdapter',
-        gffGzLocation: {
-          uri: urlTemplate,
-          locationType: 'UriLocation'
+        if (storeClass === 'JBrowse/Store/SeqFeature/VCFTabix') {
+            var adapter = {
+                type: 'VcfTabixAdapter',
+                vcfGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.tbiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                };
+            }
+            else if (jb1TrackConfig.csiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                    indexType: 'CSI',
+                };
+            }
+            else {
+                adapter.index = {
+                    location: { uri: "".concat(urlTemplate, ".tbi"), locationType: 'UriLocation' },
+                };
+            }
+            return __assign(__assign({}, jb2TrackConfig), { type: 'VariantTrack', adapter: adapter });
         }
-      };
-
-      if (jb1TrackConfig.tbiUrlTemplate) {
-        _adapter3.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-            locationType: 'UriLocation'
-          }
-        };
-      } else if (jb1TrackConfig.csiUrlTemplate) {
-        _adapter3.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-            locationType: 'UriLocation'
-          },
-          indexType: 'CSI'
-        };
-      } else {
-        _adapter3.index = {
-          location: {
-            uri: "".concat(urlTemplate, ".tbi"),
-            locationType: 'UriLocation'
-          }
-        };
-      }
-
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'FeatureTrack',
-        adapter: _adapter3
-      });
-    }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/BED') {
-      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "BED (".concat(urlTemplate, ")"), jb2TrackConfig.category);
-    }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/BEDTabix') {
-      var _adapter4 = {
-        type: 'BedTabixAdapter',
-        bedGzLocation: {
-          uri: urlTemplate,
-          locationType: 'UriLocation'
+        if (storeClass === 'JBrowse/Store/SeqFeature/VCFTribble') {
+            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, "VCFTribble (".concat(urlTemplate, ")"), jb2TrackConfig.category);
         }
-      };
-
-      if (jb1TrackConfig.tbiUrlTemplate) {
-        _adapter4.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-            locationType: 'UriLocation'
-          }
-        };
-      } else if (jb1TrackConfig.csiUrlTemplate) {
-        _adapter4.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-            locationType: 'UriLocation'
-          },
-          indexType: 'CSI'
-        };
-      } else {
-        _adapter4.index = {
-          location: {
-            uri: "".concat(urlTemplate, ".tbi"),
-            locationType: 'UriLocation'
-          }
-        };
-      }
-
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'FeatureTrack',
-        adapter: _adapter4
-      });
-    }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'FeatureTrack',
-        adapter: {
-          type: 'GtfAdapter',
-          gtfLocation: {
-            uri: urlTemplate,
-            locationType: 'UriLocation'
-          }
+        if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {
+            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: {
+                    type: 'Gff3Adapter',
+                    gffLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                } });
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {
+            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: {
+                    type: 'BigBedAdapter',
+                    bigBedLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                } });
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/GFF3Tabix') {
+            var adapter = {
+                type: 'Gff3TabixAdapter',
+                gffGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.tbiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                };
+            }
+            else if (jb1TrackConfig.csiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                    indexType: 'CSI',
+                };
+            }
+            else {
+                adapter.index = {
+                    location: { uri: "".concat(urlTemplate, ".tbi"), locationType: 'UriLocation' },
+                };
+            }
+            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: adapter });
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/BED') {
+            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, "BED (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/BEDTabix') {
+            var adapter = {
+                type: 'BedTabixAdapter',
+                bedGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.tbiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                };
+            }
+            else if (jb1TrackConfig.csiUrlTemplate) {
+                adapter.index = {
+                    location: {
+                        uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
+                        locationType: 'UriLocation',
+                    },
+                    indexType: 'CSI',
+                };
+            }
+            else {
+                adapter.index = {
+                    location: { uri: "".concat(urlTemplate, ".tbi"), locationType: 'UriLocation' },
+                };
+            }
+            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: adapter });
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {
+            return __assign(__assign({}, jb2TrackConfig), { type: 'FeatureTrack', adapter: {
+                    type: 'GtfAdapter',
+                    gtfLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                } });
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' ||
+            storeClass === 'JBrowse/Store/Sequence/StaticChunked') {
+            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, "StaticChunked (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/UnindexedFasta') {
+            return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, "UnindexedFasta (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta') {
+            var adapter = {
+                type: 'IndexedFastaAdapter',
+                fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.faiUrlTemplate) {
+                adapter.faiLocation = {
+                    uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
+                    locationType: 'UriLocation',
+                };
+            }
+            else {
+                adapter.faiLocation = {
+                    uri: "".concat(urlTemplate, ".fai"),
+                    locationType: 'UriLocation',
+                };
+            }
+            return __assign(__assign({}, jb2TrackConfig), { type: 'SequenceTrack', adapter: adapter });
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta') {
+            var adapter = {
+                type: 'BgzipFastaAdapter',
+                fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+            };
+            if (jb1TrackConfig.faiUrlTemplate) {
+                adapter.faiLocation = {
+                    uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
+                    locationType: 'UriLocation',
+                };
+            }
+            else {
+                adapter.faiLocation = {
+                    uri: "".concat(urlTemplate, ".fai"),
+                    locationType: 'UriLocation',
+                };
+            }
+            if (jb1TrackConfig.gziUrlTemplate) {
+                adapter.gziLocation = {
+                    uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
+                    locationType: 'UriLocation',
+                };
+            }
+            else {
+                adapter.gziLocation = {
+                    uri: "".concat(urlTemplate, ".gzi"),
+                    locationType: 'UriLocation',
+                };
+            }
+            return __assign(__assign({}, jb2TrackConfig), { type: 'ReferenceSequenceTrack', adapter: adapter });
+        }
+        if (storeClass === 'JBrowse/Store/SeqFeature/TwoBit') {
+            return __assign(__assign({}, jb2TrackConfig), { type: 'ReferenceSequenceTrack', adapter: {
+                    type: 'TwoBitAdapter',
+                    twoBitLocation: { uri: urlTemplate, locationType: 'UriLocation' },
+                } });
         }
-      });
     }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' || storeClass === 'JBrowse/Store/Sequence/StaticChunked') {
-      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "StaticChunked (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+    // If we don't recogize the store class, make a best effort to guess by file type
+    jb2TrackConfig.adapter = (0, tracks_1.guessAdapter)({ uri: urlTemplate, locationType: 'UriLocation' }, undefined, urlTemplate);
+    if (!jb2TrackConfig.adapter) {
+        throw new Error('Could not determine adapter');
     }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/UnindexedFasta') {
-      return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, "UnindexedFasta (".concat(urlTemplate, ")"), jb2TrackConfig.category);
+    if (jb2TrackConfig.adapter.type === tracks_1.UNSUPPORTED) {
+        return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
     }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta') {
-      var _adapter5 = {
-        type: 'IndexedFastaAdapter',
-        fastaLocation: {
-          uri: urlTemplate,
-          locationType: 'UriLocation'
-        }
-      };
-
-      if (jb1TrackConfig.faiUrlTemplate) {
-        _adapter5.faiLocation = {
-          uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-          locationType: 'UriLocation'
-        };
-      } else {
-        _adapter5.faiLocation = {
-          uri: "".concat(urlTemplate, ".fai"),
-          locationType: 'UriLocation'
-        };
-      }
-
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'SequenceTrack',
-        adapter: _adapter5
-      });
+    if (jb2TrackConfig.adapter.type === tracks_1.UNKNOWN) {
+        return (0, tracks_1.generateUnknownTrackConf)(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
     }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta') {
-      var _adapter6 = {
-        type: 'BgzipFastaAdapter',
-        fastaLocation: {
-          uri: urlTemplate,
-          locationType: 'UriLocation'
+    jb2TrackConfig.type = (0, tracks_1.guessTrackType)(jb2TrackConfig.adapter.type);
+    if (jb2TrackConfig.type === 'QuantitativeTrack') {
+        if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
+            jb2TrackConfig.defaultRendering = 'xyplot';
         }
-      };
-
-      if (jb1TrackConfig.faiUrlTemplate) {
-        _adapter6.faiLocation = {
-          uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-          locationType: 'UriLocation'
-        };
-      } else {
-        _adapter6.faiLocation = {
-          uri: "".concat(urlTemplate, ".fai"),
-          locationType: 'UriLocation'
-        };
-      }
-
-      if (jb1TrackConfig.gziUrlTemplate) {
-        _adapter6.gziLocation = {
-          uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
-          locationType: 'UriLocation'
-        };
-      } else {
-        _adapter6.gziLocation = {
-          uri: "".concat(urlTemplate, ".gzi"),
-          locationType: 'UriLocation'
-        };
-      }
-
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'ReferenceSequenceTrack',
-        adapter: _adapter6
-      });
-    }
-
-    if (storeClass === 'JBrowse/Store/SeqFeature/TwoBit') {
-      return _objectSpread(_objectSpread({}, jb2TrackConfig), {}, {
-        type: 'ReferenceSequenceTrack',
-        adapter: {
-          type: 'TwoBitAdapter',
-          twoBitLocation: {
-            uri: urlTemplate,
-            locationType: 'UriLocation'
-          }
+        else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
+            jb2TrackConfig.defaultRendering = 'density';
         }
-      });
-    }
-  } // If we don't recogize the store class, make a best effort to guess by file type
-
-
-  jb2TrackConfig.adapter = (0, _tracks.guessAdapter)({
-    uri: urlTemplate,
-    locationType: 'UriLocation'
-  }, undefined, urlTemplate);
-
-  if (!jb2TrackConfig.adapter) {
-    throw new Error('Could not determine adapter');
-  }
-
-  if (jb2TrackConfig.adapter.type === _tracks.UNSUPPORTED) {
-    return (0, _tracks.generateUnsupportedTrackConf)(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
-  }
-
-  if (jb2TrackConfig.adapter.type === _tracks.UNKNOWN) {
-    return (0, _tracks.generateUnknownTrackConf)(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
-  }
-
-  jb2TrackConfig.type = (0, _tracks.guessTrackType)(jb2TrackConfig.adapter.type);
-
-  if (jb2TrackConfig.type === 'QuantitativeTrack') {
-    if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
-      jb2TrackConfig.defaultRendering = 'xyplot';
-    } else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
-      jb2TrackConfig.defaultRendering = 'density';
     }
-  }
-
-  return jb2TrackConfig;
+    return jb2TrackConfig;
 }
-
+exports.convertTrackConfig = convertTrackConfig;
 function generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig) {
-  var jb1Features = jb1TrackConfig.features || [];
-  var jb2Features = jb1Features.map(function (feature) {
-    var jb2Feature = JSON.parse(JSON.stringify(feature));
-    jb2Feature.refName = feature.seq_id;
-    jb2Feature.uniqueId = "".concat(feature.seq_id, ":").concat(feature.start, "-").concat(feature.end, ":").concat(feature.name || '');
-    return jb2Feature;
-  });
-  jb2TrackConfig.adapter = {
-    type: 'FromConfigAdapter',
-    features: jb2Features
-  };
-  jb2TrackConfig.type = 'FeatureTrack';
-  return jb2TrackConfig;
-}
-
-function createRefSeqsAdapter(_x) {
-  return _createRefSeqsAdapter.apply(this, arguments);
+    var jb1Features = jb1TrackConfig.features || [];
+    var jb2Features = jb1Features.map(function (feature) {
+        var jb2Feature = JSON.parse(JSON.stringify(feature));
+        jb2Feature.refName = feature.seq_id;
+        jb2Feature.uniqueId = "".concat(feature.seq_id, ":").concat(feature.start, "-").concat(feature.end, ":").concat(feature.name || '');
+        return jb2Feature;
+    });
+    jb2TrackConfig.adapter = {
+        type: 'FromConfigAdapter',
+        features: jb2Features,
+    };
+    jb2TrackConfig.type = 'FeatureTrack';
+    return jb2TrackConfig;
 }
-
-function _createRefSeqsAdapter() {
-  _createRefSeqsAdapter = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(refSeqs) {
-    var refSeqsJson, refSeqsData;
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            if (typeof refSeqs === 'string') {
-              // assume refSeqs is a url if it is string
-              refSeqs = {
-                url: refSeqs
-              };
-            } // check refseq urls
-
-
-            if (!refSeqs.url) {
-              _context.next = 15;
-              break;
-            }
-
-            if (!refSeqs.url.match(/.fai$/)) {
-              _context.next = 4;
-              break;
+function createRefSeqsAdapter(refSeqs) {
+    return __awaiter(this, void 0, void 0, function () {
+        var refSeqsJson, refSeqsData;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    if (typeof refSeqs === 'string') {
+                        // assume refSeqs is a url if it is string
+                        refSeqs = {
+                            url: refSeqs,
+                        };
+                    }
+                    if (!refSeqs.url) return [3 /*break*/, 2];
+                    if (refSeqs.url.match(/.fai$/)) {
+                        return [2 /*return*/, {
+                                type: 'IndexedFastaAdapter',
+                                fastaLocation: {
+                                    uri: refSeqs.url.slice(0, -4),
+                                    locationType: 'UriLocation',
+                                },
+                                faiLocation: {
+                                    uri: refSeqs.url,
+                                    locationType: 'UriLocation',
+                                },
+                            }];
+                    }
+                    if (refSeqs.url.match(/.2bit$/)) {
+                        return [2 /*return*/, {
+                                type: 'TwoBitAdapter',
+                                twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },
+                            }];
+                    }
+                    if (refSeqs.url.match(/.fa$/)) {
+                        throw new Error('Unindexed FASTA adapter not available');
+                    }
+                    if (refSeqs.url.match(/.sizes/)) {
+                        throw new Error('chromosome SIZES adapter not available');
+                    }
+                    return [4 /*yield*/, (0, io_1.openLocation)({
+                            uri: refSeqs.url,
+                            locationType: 'UriLocation',
+                        }).readFile('utf8')];
+                case 1:
+                    refSeqsJson = _a.sent();
+                    refSeqsData = JSON.parse(refSeqsJson);
+                    return [2 /*return*/, refSeqAdapterFromConfig(refSeqsData)];
+                case 2:
+                    if ('data' in refSeqs) {
+                        return [2 /*return*/, refSeqAdapterFromConfig(refSeqs.data || [])];
+                    }
+                    throw new Error("Could not determine adapter for JBrowse1 refSeqs: ".concat(refSeqs.url || JSON.stringify(refSeqs)));
             }
-
-            return _context.abrupt("return", {
-              type: 'IndexedFastaAdapter',
-              fastaLocation: {
-                uri: refSeqs.url.slice(0, -4),
-                locationType: 'UriLocation'
-              },
-              faiLocation: {
-                uri: refSeqs.url,
-                locationType: 'UriLocation'
-              }
-            });
-
-          case 4:
-            if (!refSeqs.url.match(/.2bit$/)) {
-              _context.next = 6;
-              break;
-            }
-
-            return _context.abrupt("return", {
-              type: 'TwoBitAdapter',
-              twoBitLocation: {
-                uri: refSeqs.url,
-                locationType: 'UriLocation'
-              }
-            });
-
-          case 6:
-            if (!refSeqs.url.match(/.fa$/)) {
-              _context.next = 8;
-              break;
-            }
-
-            throw new Error('Unindexed FASTA adapter not available');
-
-          case 8:
-            if (!refSeqs.url.match(/.sizes/)) {
-              _context.next = 10;
-              break;
-            }
-
-            throw new Error('chromosome SIZES adapter not available');
-
-          case 10:
-            _context.next = 12;
-            return (0, _io.openLocation)({
-              uri: refSeqs.url,
-              locationType: 'UriLocation'
-            }).readFile('utf8');
-
-          case 12:
-            refSeqsJson = _context.sent;
-            refSeqsData = JSON.parse(refSeqsJson);
-            return _context.abrupt("return", refSeqAdapterFromConfig(refSeqsData));
-
-          case 15:
-            if (!('data' in refSeqs)) {
-              _context.next = 17;
-              break;
-            }
-
-            return _context.abrupt("return", refSeqAdapterFromConfig(refSeqs.data || []));
-
-          case 17:
-            throw new Error("Could not determine adapter for JBrowse1 refSeqs: ".concat(refSeqs.url || JSON.stringify(refSeqs)));
-
-          case 18:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  }));
-  return _createRefSeqsAdapter.apply(this, arguments);
+        });
+    });
 }
-
+exports.createRefSeqsAdapter = createRefSeqsAdapter;
 function refSeqAdapterFromConfig(refSeqsData) {
-  var features = refSeqsData.map(function (refSeq) {
+    var features = refSeqsData.map(function (refSeq) { return ({
+        refName: refSeq.name,
+        uniqueId: refSeq.name,
+        start: refSeq.start,
+        end: refSeq.end,
+    }); });
     return {
-      refName: refSeq.name,
-      uniqueId: refSeq.name,
-      start: refSeq.start,
-      end: refSeq.end
+        type: 'FromConfigAdapter',
+        features: features,
     };
-  });
-  return {
-    type: 'FromConfigAdapter',
-    features: features
-  };
-}
+}
+//# sourceMappingURL=jb1ToJb2.js.map