@apollo-annotation/jbrowse-plugin-apollo 0.1.19 → 0.1.20

package/dist/jbrowse-plugin-apollo.umd.development.js

@@ -2,7 +2,7 @@
 	typeof exports === 'object' && typeof module !== 'undefined' ? factory(exports, require('@jbrowse/core/Plugin'), require('@jbrowse/core/util'), require('@jbrowse/core/configuration'), require('@jbrowse/core/pluggableElementTypes'), require('@mui/material/utils'), require('react/jsx-runtime'), require('mobx'), require('mobx-state-tree'), require('@mui/material'), require('@mui/material/InputAdornment'), require('@mui/material/LinearProgress'), require('react'), require('@jbrowse/core/ui'), require('mobx-react'), require('tss-react/mui'), require('@jbrowse/core/util/types/mst'), require('@jbrowse/core/util/io'), require('@mui/material/Checkbox'), require('@mui/material/FormControlLabel'), require('@mui/x-data-grid'), require('@jbrowse/core/pluggableElementTypes/AdapterType'), require('@jbrowse/core/data_adapters/BaseAdapter'), require('@jbrowse/core/util/rxjs'), require('@jbrowse/core/util/tracks')) :
 	typeof define === 'function' && define.amd ? define(['exports', '@jbrowse/core/Plugin', '@jbrowse/core/util', '@jbrowse/core/configuration', '@jbrowse/core/pluggableElementTypes', '@mui/material/utils', 'react/jsx-runtime', 'mobx', 'mobx-state-tree', '@mui/material', '@mui/material/InputAdornment', '@mui/material/LinearProgress', 'react', '@jbrowse/core/ui', 'mobx-react', 'tss-react/mui', '@jbrowse/core/util/types/mst', '@jbrowse/core/util/io', '@mui/material/Checkbox', '@mui/material/FormControlLabel', '@mui/x-data-grid', '@jbrowse/core/pluggableElementTypes/AdapterType', '@jbrowse/core/data_adapters/BaseAdapter', '@jbrowse/core/util/rxjs', '@jbrowse/core/util/tracks'], factory) :
 	(global = typeof globalThis !== 'undefined' ? globalThis : global || self, factory(global.JBrowsePluginApollo = {}, global.JBrowseExports["@jbrowse/core/Plugin"], global.JBrowseExports["@jbrowse/core/util"], global.JBrowseExports["@jbrowse/core/configuration"], global.JBrowseExports["@jbrowse/core/pluggableElementTypes"], global.JBrowseExports["@mui/material/utils"], global.JBrowseExports["react/jsx-runtime"], global.JBrowseExports.mobx, global.JBrowseExports["mobx-state-tree"], global.JBrowseExports["@mui/material"], global.JBrowseExports["@mui/material/InputAdornment"], global.JBrowseExports["@mui/material/LinearProgress"], global.JBrowseExports.react, global.JBrowseExports["@jbrowse/core/ui"], global.JBrowseExports["mobx-react"], global.JBrowseExports["tss-react/mui"], global.JBrowseExports["@jbrowse/core/util/types/mst"], global.JBrowseExports["@jbrowse/core/util/io"], global.JBrowseExports["@mui/material/Checkbox"], global.JBrowseExports["@mui/material/FormControlLabel"], global.JBrowseExports["@mui/x-data-grid"], global.JBrowseExports["@jbrowse/core/pluggableElementTypes/AdapterType"], global.JBrowseExports["@jbrowse/core/data_adapters/BaseAdapter"], global.JBrowseExports["@jbrowse/core/util/rxjs"], global.JBrowseExports["@jbrowse/core/util/tracks"]));
-})(this, (function (exports, require$$1$2, require$$1$3, configuration, pluggableElementTypes, require$$0$1, require$$2$1, mobx, require$$1$4, material, InputAdornment, LinearProgress, React, ui, mobxReact, mui, mst, io, Checkbox, FormControlLabel, xDataGrid, AdapterType, BaseAdapter, rxjs, tracks) { 'use strict';
+})(this, (function (exports, require$$1$1, require$$1$2, configuration, pluggableElementTypes, require$$0$2, require$$2$1, mobx, require$$1$3, material, InputAdornment, LinearProgress, React, ui, mobxReact, mui, mst, io, Checkbox, FormControlLabel, xDataGrid, AdapterType, BaseAdapter, rxjs, tracks) { 'use strict';
 
 	function _interopDefaultLegacy (e) { return e && typeof e === 'object' && 'default' in e ? e : { 'default': e }; }
 
@@ -24,11 +24,11 @@
 		return n;
 	}
 
-	var require$$1__default = /*#__PURE__*/_interopDefaultLegacy(require$$1$2);
-	var require$$1__default$1 = /*#__PURE__*/_interopDefaultLegacy(require$$1$3);
-	var require$$0__default = /*#__PURE__*/_interopDefaultLegacy(require$$0$1);
+	var require$$1__default = /*#__PURE__*/_interopDefaultLegacy(require$$1$1);
+	var require$$1__default$1 = /*#__PURE__*/_interopDefaultLegacy(require$$1$2);
+	var require$$0__default = /*#__PURE__*/_interopDefaultLegacy(require$$0$2);
 	var require$$2__default = /*#__PURE__*/_interopDefaultLegacy(require$$2$1);
-	var require$$1__default$2 = /*#__PURE__*/_interopDefaultLegacy(require$$1$4);
+	var require$$1__default$2 = /*#__PURE__*/_interopDefaultLegacy(require$$1$3);
 	var InputAdornment__default = /*#__PURE__*/_interopDefaultLegacy(InputAdornment);
 	var LinearProgress__default = /*#__PURE__*/_interopDefaultLegacy(LinearProgress);
 	var React__default = /*#__PURE__*/_interopDefaultLegacy(React);
@@ -1419,7 +1419,7 @@
 		'default': tslib_es6
 	};
 
-	var require$$0 = /*@__PURE__*/getAugmentedNamespace(tslib_es6$1);
+	var require$$0$1 = /*@__PURE__*/getAugmentedNamespace(tslib_es6$1);
 
 	var ApolloPlugin$4 = {};
 
@@ -1427,8 +1427,8 @@
 	  value: true
 	});
 	ApolloPlugin$4.ApolloPlugin = void 0;
-	var tslib_1$6 = require$$0;
-	var Plugin_1$1 = /*#__PURE__*/tslib_1$6.__importDefault(require$$1__default["default"]);
+	var tslib_1$7 = require$$0$1;
+	var Plugin_1$1 = /*#__PURE__*/tslib_1$7.__importDefault(require$$1__default["default"]);
 	var ApolloPlugin$3 = /*#__PURE__*/function (_Plugin_1$default) {
 	  _inherits(ApolloPlugin, _Plugin_1$default);
 	  var _super = /*#__PURE__*/_createSuper(ApolloPlugin);
@@ -3832,8 +3832,8 @@
 	});
 	FeatureChange$3.FeatureChange = void 0;
 	FeatureChange$3.isFeatureChange = isFeatureChange$1;
-	var tslib_1$5 = require$$0;
-	var bson_objectid_1$2 = /*#__PURE__*/tslib_1$5.__importDefault(objectid);
+	var tslib_1$6 = require$$0$1;
+	var bson_objectid_1$3 = /*#__PURE__*/tslib_1$6.__importDefault(objectid);
 	var AssemblySpecificChange_1$1 = AssemblySpecificChange$3;
 	// eslint-disable-next-line @typescript-eslint/no-explicit-any
 	function isFeatureChange$1(thing) {
@@ -3923,7 +3923,7 @@
 	  }, {
 	    key: "generateNewIds",
 	    value: function generateNewIds(feature, featureIds) {
-	      var newId = new bson_objectid_1$2["default"]().toHexString();
+	      var newId = new bson_objectid_1$3["default"]().toHexString();
 	      featureIds.push(newId);
 	      var children = {};
 	      if (feature.children) {
@@ -4106,7 +4106,7 @@
 	  Object.defineProperty(exports, "__esModule", {
 	    value: true
 	  });
-	  var tslib_1 = require$$0;
+	  var tslib_1 = require$$0$1;
 	  tslib_1.__exportStar(ApolloPlugin$4, exports);
 	  tslib_1.__exportStar(AssemblySpecificChange$3, exports);
 	  tslib_1.__exportStar(Change$3, exports);
@@ -4135,8 +4135,8 @@
 	  value: true
 	});
 	ApolloPlugin$2.ApolloPlugin = void 0;
-	var tslib_1$4 = require$$0;
-	var Plugin_1 = /*#__PURE__*/tslib_1$4.__importDefault(require$$1__default["default"]);
+	var tslib_1$5 = require$$0$1;
+	var Plugin_1 = /*#__PURE__*/tslib_1$5.__importDefault(require$$1__default["default"]);
 	var ApolloPlugin$1 = /*#__PURE__*/function (_Plugin_1$default) {
 	  _inherits(ApolloPlugin, _Plugin_1$default);
 	  var _super = /*#__PURE__*/_createSuper(ApolloPlugin);
@@ -4404,8 +4404,8 @@
 	});
 	FeatureChange$1.FeatureChange = void 0;
 	FeatureChange$1.isFeatureChange = isFeatureChange;
-	var tslib_1$3 = require$$0;
-	var bson_objectid_1$1 = /*#__PURE__*/tslib_1$3.__importDefault(objectid);
+	var tslib_1$4 = require$$0$1;
+	var bson_objectid_1$2 = /*#__PURE__*/tslib_1$4.__importDefault(objectid);
 	var AssemblySpecificChange_1 = AssemblySpecificChange$1;
 	// eslint-disable-next-line @typescript-eslint/no-explicit-any
 	function isFeatureChange(thing) {
@@ -4495,7 +4495,7 @@
 	  }, {
 	    key: "generateNewIds",
 	    value: function generateNewIds(feature, featureIds) {
-	      var newId = new bson_objectid_1$1["default"]().toHexString();
+	      var newId = new bson_objectid_1$2["default"]().toHexString();
 	      featureIds.push(newId);
 	      var children = {};
 	      if (feature.children) {
@@ -4678,7 +4678,7 @@
 	  Object.defineProperty(exports, "__esModule", {
 	    value: true
 	  });
-	  var tslib_1 = require$$0;
+	  var tslib_1 = require$$0$1;
 	  tslib_1.__exportStar(ApolloPlugin$2, exports);
 	  tslib_1.__exportStar(AssemblySpecificChange$1, exports);
 	  tslib_1.__exportStar(Change$1, exports);
@@ -4739,9 +4739,9 @@
 	  value: true
 	});
 	gff3ToAnnotationFeature$1.gff3ToAnnotationFeature = gff3ToAnnotationFeature;
-	var tslib_1$2 = require$$0;
-	var util_1$2 = require$$1__default$1["default"];
-	var bson_objectid_1 = /*#__PURE__*/tslib_1$2.__importDefault(objectid);
+	var tslib_1$3 = require$$0$1;
+	var util_1$3 = require$$1__default$1["default"];
+	var bson_objectid_1$1 = /*#__PURE__*/tslib_1$3.__importDefault(objectid);
 	var gffReservedKeys_1 = gffReservedKeys;
 	function gff3ToAnnotationFeature(gff3Feature, refSeq, featureIds) {
 	  var _gff3Feature = _slicedToArray(gff3Feature, 1),
@@ -4770,7 +4770,7 @@
 	  var convertedChildren = convertChildren(gff3Feature, refSeq, featureIds);
 	  var convertedAttributes = convertFeatureAttributes(gff3Feature);
 	  var feature = {
-	    _id: new bson_objectid_1["default"]().toHexString(),
+	    _id: new bson_objectid_1$1["default"]().toHexString(),
 	    refSeq: refSeq !== null && refSeq !== void 0 ? refSeq : refName,
 	    type: type,
 	    min: min,
@@ -4849,13 +4849,12 @@
 	    var _sources = _slicedToArray(sources, 1),
 	      source = _sources[0];
 	    if (sources.length > 1) {
-	      var sourceSet = _construct(Set, _toConsumableArray(sources));
+	      var sourceSet = new Set(sources);
 	      source = _toConsumableArray(sourceSet).join(',');
 	    }
 	    convertedAttributes.gff_source = [source];
 	  }
 	  if (attributesCollections.length > 0) {
-	    var newAttributes = {};
 	    var _iterator = _createForOfIteratorHelper(attributesCollections),
 	      _step;
 	    try {
@@ -4869,9 +4868,9 @@
 	            continue;
 	          }
 	          var newKey = (0, gffReservedKeys_1.isGFFReservedAttribute)(key) ? gffReservedKeys_1.gffToInternal[key] : key;
-	          var existingVal = newAttributes[newKey];
+	          var existingVal = convertedAttributes[newKey];
 	          if (existingVal) {
-	            var valSet = _construct(Set, _toConsumableArray(existingVal).concat(_toConsumableArray(val)));
+	            var valSet = new Set([].concat(_toConsumableArray(existingVal), _toConsumableArray(val)));
 	            convertedAttributes[newKey] = _toConsumableArray(valSet);
 	          } else {
 	            convertedAttributes[newKey] = val;
@@ -4911,7 +4910,7 @@
 	      var childFeature = _step2.value;
 	      var _childFeature = _slicedToArray(childFeature, 1),
 	        firstChildFeatureLocation = _childFeature[0];
-	      if (firstChildFeatureLocation.type === 'three_prime_UTR' || firstChildFeatureLocation.type === 'five_prime_UTR') {
+	      if (firstChildFeatureLocation.type === 'three_prime_UTR' || firstChildFeatureLocation.type === 'five_prime_UTR' || firstChildFeatureLocation.type === 'intron' || firstChildFeatureLocation.type === 'start_codon' || firstChildFeatureLocation.type === 'stop_codon') {
 	        continue;
 	      }
 	      if (firstChildFeatureLocation.type === 'CDS') {
@@ -4983,7 +4982,7 @@
 	      return false;
 	    }
 	    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-	    return (0, util_1$2.doesIntersect2)(loc.start, loc.end, nextLoc.start, nextLoc.end);
+	    return (0, util_1$3.doesIntersect2)(loc.start, loc.end, nextLoc.start, nextLoc.end);
 	  });
 	  // If no overlaps, assume it's a single CDS feature
 	  if (!overlapping) {
@@ -4998,23 +4997,25 @@
 	  var _iterator4 = _createForOfIteratorHelper(cdsLocations),
 	    _step4;
 	  try {
-	    for (_iterator4.s(); !(_step4 = _iterator4.n()).done;) {
+	    var _loop = function _loop() {
 	      var location = _step4.value;
 	      var lastGroup = groupedLocations.at(-1);
 	      if (!lastGroup) {
 	        groupedLocations.push([location]);
-	        continue;
-	      }
-	      var lastGroupLastLocation = lastGroup.at(-1);
-	      if (!lastGroupLastLocation) {
-	        throw new Error('Got group with no locations');
+	        return 1; // continue
 	      }
-	      if ((0, util_1$2.doesIntersect2)( /* eslint-disable @typescript-eslint/no-non-null-assertion */
-	      lastGroupLastLocation.start, lastGroupLastLocation.end, location.start, location.end)) {
+	      var overlaps = lastGroup.some(function (lastGroupLoc) {
+	        return (0, util_1$3.doesIntersect2)( /* eslint-disable @typescript-eslint/no-non-null-assertion */
+	        lastGroupLoc.start, lastGroupLoc.end, location.start, location.end);
+	      });
+	      if (overlaps) {
 	        groupedLocations.push([location]);
 	      } else {
 	        lastGroup.push(location);
 	      }
+	    };
+	    for (_iterator4.s(); !(_step4 = _iterator4.n()).done;) {
+	      if (_loop()) continue;
 	    }
 	  } catch (err) {
 	    _iterator4.e(err);
@@ -5031,7 +5032,7 @@
 	  Object.defineProperty(exports, "__esModule", {
 	    value: true
 	  });
-	  var tslib_1 = require$$0;
+	  var tslib_1 = require$$0$1;
 	  tslib_1.__exportStar(gffReservedKeys, exports);
 	  tslib_1.__exportStar(gff3ToAnnotationFeature$1, exports);
 	})(GFF3);
@@ -5517,12 +5518,12 @@
 	        var _changes = _slicedToArray(changes, 1),
 	          _changes$ = _changes[0],
 	          assemblyName = _changes$.assemblyName,
-	          fileId = _changes$.fileId;
+	          fileIds = _changes$.fileIds;
 	        return {
 	          typeName: typeName,
 	          assembly: assembly,
 	          assemblyName: assemblyName,
-	          fileId: fileId
+	          fileIds: fileIds
 	        };
 	      }
 	      return {
@@ -5540,7 +5541,7 @@
 	    key: "executeOnServer",
 	    value: function () {
 	      var _executeOnServer = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee(backend) {
-	        var assemblyModel, fileModel, filesService, user, assembly, changes, logger, _iterator2, _step2, _logger$debug, _logger$debug2, _logger$debug3, _logger$debug4, change, assemblyName, fileId, FILE_UPLOAD_FOLDER, fileDoc, assemblyDoc, _yield$assemblyModel$, _yield$assemblyModel$2, newAssemblyDoc, featureStream, _iteratorAbruptCompletion, _didIteratorError, _iteratorError, _iterator, _step, f, _logger$verbose, gff3Feature;
+	        var assemblyModel, fileModel, filesService, user, assembly, changes, logger, _iterator2, _step2, _logger$debug, _logger$debug2, _logger$debug3, _logger$debug4, change, assemblyName, fileIds, fileId, FILE_UPLOAD_FOLDER, fileDoc, assemblyDoc, _yield$assemblyModel$, _yield$assemblyModel$2, newAssemblyDoc, featureStream, _iteratorAbruptCompletion, _didIteratorError, _iteratorError, _iterator, _step, f, _logger$verbose, gff3Feature;
 	        return _regeneratorRuntime().wrap(function _callee$(_context) {
 	          while (1) switch (_context.prev = _context.next) {
 	            case 0:
@@ -5551,50 +5552,52 @@
 	              _iterator2.s();
 	            case 5:
 	              if ((_step2 = _iterator2.n()).done) {
-	                _context.next = 66;
+	                _context.next = 67;
 	                break;
 	              }
 	              change = _step2.value;
-	              assemblyName = change.assemblyName, fileId = change.fileId;
+	              assemblyName = change.assemblyName, fileIds = change.fileIds;
+	              fileId = fileIds.fa;
 	              FILE_UPLOAD_FOLDER = process.env.FILE_UPLOAD_FOLDER;
 	              if (FILE_UPLOAD_FOLDER) {
-	                _context.next = 11;
+	                _context.next = 12;
 	                break;
 	              }
 	              throw new Error('No FILE_UPLOAD_FOLDER found in .env file');
-	            case 11:
-	              _context.next = 13;
+	            case 12:
+	              _context.next = 14;
 	              return fileModel.findById(fileId).exec();
-	            case 13:
+	            case 14:
 	              fileDoc = _context.sent;
 	              if (fileDoc) {
-	                _context.next = 16;
+	                _context.next = 17;
 	                break;
 	              }
 	              throw new Error("File \"".concat(fileId, "\" not found in Mongo"));
-	            case 16:
+	            case 17:
 	              (_logger$debug = logger.debug) === null || _logger$debug === void 0 || _logger$debug.call(logger, "FileId \"".concat(fileId, "\", checksum \"").concat(fileDoc.checksum, "\""));
 	              // Check and add new assembly
-	              _context.next = 19;
+	              _context.next = 20;
 	              return assemblyModel.findOne({
 	                name: assemblyName
 	              }).exec();
-	            case 19:
+	            case 20:
 	              assemblyDoc = _context.sent;
 	              if (!assemblyDoc) {
-	                _context.next = 22;
+	                _context.next = 23;
 	                break;
 	              }
 	              throw new Error("Assembly \"".concat(assemblyName, "\" already exists"));
-	            case 22:
-	              _context.next = 24;
+	            case 23:
+	              _context.next = 25;
 	              return assemblyModel.create([{
 	                _id: assembly,
 	                name: assemblyName,
 	                user: user,
-	                status: -1
+	                status: -1,
+	                fileId: fileId
 	              }]);
-	            case 24:
+	            case 25:
 	              _yield$assemblyModel$ = _context.sent;
 	              _yield$assemblyModel$2 = _slicedToArray(_yield$assemblyModel$, 1);
 	              newAssemblyDoc = _yield$assemblyModel$2[0];
@@ -5602,81 +5605,81 @@
 	              (_logger$debug3 = logger.debug) === null || _logger$debug3 === void 0 || _logger$debug3.call(logger, "File type: \"".concat(fileDoc.type, "\""));
 	              // Add refSeqs
 	              // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-	              _context.next = 31;
+	              _context.next = 32;
 	              return this.addRefSeqIntoDb(fileDoc, newAssemblyDoc._id.toString(), backend);
-	            case 31:
+	            case 32:
 	              // Loop all features
 	              (_logger$debug4 = logger.debug) === null || _logger$debug4 === void 0 || _logger$debug4.call(logger, "**************** LOOPATAAN KAIKKI FEATURET SEURAAVAKSI File type: \"".concat(fileDoc.type, "\""));
 	              featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc));
 	              _iteratorAbruptCompletion = false;
 	              _didIteratorError = false;
-	              _context.prev = 35;
+	              _context.prev = 36;
 	              _iterator = _asyncIterator(featureStream);
-	            case 37:
-	              _context.next = 39;
+	            case 38:
+	              _context.next = 40;
 	              return _iterator.next();
-	            case 39:
+	            case 40:
 	              if (!(_iteratorAbruptCompletion = !(_step = _context.sent).done)) {
-	                _context.next = 48;
+	                _context.next = 49;
 	                break;
 	              }
 	              f = _step.value;
 	              gff3Feature = f;
 	              (_logger$verbose = logger.verbose) === null || _logger$verbose === void 0 || _logger$verbose.call(logger, "ENTRY=".concat(JSON.stringify(gff3Feature)));
 	              // Add new feature into database
-	              _context.next = 45;
+	              _context.next = 46;
 	              return this.addFeatureIntoDb(gff3Feature, backend);
-	            case 45:
+	            case 46:
 	              _iteratorAbruptCompletion = false;
-	              _context.next = 37;
+	              _context.next = 38;
 	              break;
-	            case 48:
-	              _context.next = 54;
+	            case 49:
+	              _context.next = 55;
 	              break;
-	            case 50:
-	              _context.prev = 50;
-	              _context.t0 = _context["catch"](35);
+	            case 51:
+	              _context.prev = 51;
+	              _context.t0 = _context["catch"](36);
 	              _didIteratorError = true;
 	              _iteratorError = _context.t0;
-	            case 54:
-	              _context.prev = 54;
+	            case 55:
 	              _context.prev = 55;
+	              _context.prev = 56;
 	              if (!(_iteratorAbruptCompletion && _iterator["return"] != null)) {
-	                _context.next = 59;
+	                _context.next = 60;
 	                break;
 	              }
-	              _context.next = 59;
+	              _context.next = 60;
 	              return _iterator["return"]();
-	            case 59:
-	              _context.prev = 59;
+	            case 60:
+	              _context.prev = 60;
 	              if (!_didIteratorError) {
-	                _context.next = 62;
+	                _context.next = 63;
 	                break;
 	              }
 	              throw _iteratorError;
-	            case 62:
-	              return _context.finish(59);
 	            case 63:
-	              return _context.finish(54);
+	              return _context.finish(60);
 	            case 64:
+	              return _context.finish(55);
+	            case 65:
 	              _context.next = 5;
 	              break;
-	            case 66:
-	              _context.next = 71;
+	            case 67:
+	              _context.next = 72;
 	              break;
-	            case 68:
-	              _context.prev = 68;
+	            case 69:
+	              _context.prev = 69;
 	              _context.t1 = _context["catch"](3);
 	              _iterator2.e(_context.t1);
-	            case 71:
-	              _context.prev = 71;
+	            case 72:
+	              _context.prev = 72;
 	              _iterator2.f();
-	              return _context.finish(71);
-	            case 74:
+	              return _context.finish(72);
+	            case 75:
 	            case "end":
 	              return _context.stop();
 	          }
-	        }, _callee, this, [[3, 68, 71, 74], [35, 50, 54, 64], [55,, 59, 63]]);
+	        }, _callee, this, [[3, 69, 72, 75], [36, 51, 55, 65], [56,, 60, 64]]);
 	      }));
 	      function executeOnServer(_x) {
 	        return _executeOnServer.apply(this, arguments);
@@ -15164,7 +15167,7 @@
 		BgzipIndexedFasta: BgzipIndexedFasta
 	};
 
-	var require$$1$1 = /*@__PURE__*/getAugmentedNamespace(esm);
+	var require$$0 = /*@__PURE__*/getAugmentedNamespace(esm);
 
 	var require$$2 = /*@__PURE__*/getAugmentedNamespace(esm$1);
 
@@ -15176,7 +15179,7 @@
 	AddAssemblyFromExternalChange$1.AddAssemblyFromExternalChange = void 0;
 	/* eslint-disable @typescript-eslint/require-await */
 	var common_1$f = dist$1;
-	var indexedfasta_1 = require$$1$1;
+	var indexedfasta_1$1 = require$$0;
 	var generic_filehandle_1 = require$$2;
 	var AddAssemblyFromExternalChange = /*#__PURE__*/function (_common_1$AssemblySpe) {
 	  _inherits(AddAssemblyFromExternalChange, _common_1$AssemblySpe);
@@ -15247,7 +15250,7 @@
 	              change = _step.value;
 	              assemblyName = change.assemblyName, externalLocation = change.externalLocation;
 	              fa = externalLocation.fa, fai = externalLocation.fai, gzi = externalLocation.gzi;
-	              sequenceAdapter = gzi ? new indexedfasta_1.BgzipIndexedFasta({
+	              sequenceAdapter = gzi ? new indexedfasta_1$1.BgzipIndexedFasta({
 	                fasta: new generic_filehandle_1.RemoteFile(fa, {
 	                  fetch: fetch
 	                }),
@@ -15257,7 +15260,7 @@
 	                gzi: new generic_filehandle_1.RemoteFile(gzi, {
 	                  fetch: fetch
 	                })
-	              }) : new indexedfasta_1.IndexedFasta({
+	              }) : new indexedfasta_1$1.IndexedFasta({
 	                fasta: new generic_filehandle_1.RemoteFile(fa, {
 	                  fetch: fetch
 	                }),
@@ -15412,6 +15415,7 @@
 	  value: true
 	});
 	AddAssemblyFromFileChange$1.AddAssemblyFromFileChange = void 0;
+	var indexedfasta_1 = require$$0;
 	var FromFileBaseChange_1$1 = FromFileBaseChange$1;
 	var AddAssemblyFromFileChange = /*#__PURE__*/function (_FromFileBaseChange_) {
 	  _inherits(AddAssemblyFromFileChange, _FromFileBaseChange_);
@@ -15440,12 +15444,12 @@
 	        var _changes = _slicedToArray(changes, 1),
 	          _changes$ = _changes[0],
 	          assemblyName = _changes$.assemblyName,
-	          fileId = _changes$.fileId;
+	          fileIds = _changes$.fileIds;
 	        return {
 	          typeName: typeName,
 	          assembly: assembly,
 	          assemblyName: assemblyName,
-	          fileId: fileId
+	          fileIds: fileIds
 	        };
 	      }
 	      return {
@@ -15463,110 +15467,251 @@
 	    key: "executeOnServer",
 	    value: function () {
 	      var _executeOnServer = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee(backend) {
-	        var assemblyModel, fileModel, user, assembly, changes, logger, _iterator, _step, _logger$debug, _logger$debug2, _logger$debug3, change, assemblyName, fileId, FILE_UPLOAD_FOLDER, fileDoc, assemblyDoc, _yield$assemblyModel$, _yield$assemblyModel$2, newAssemblyDoc;
+	        var changes, _iterator, _step, change, assemblyName, fileIds;
 	        return _regeneratorRuntime().wrap(function _callee$(_context) {
 	          while (1) switch (_context.prev = _context.next) {
 	            case 0:
-	              assemblyModel = backend.assemblyModel, fileModel = backend.fileModel, user = backend.user;
-	              assembly = this.assembly, changes = this.changes, logger = this.logger;
+	              changes = this.changes;
 	              _iterator = _createForOfIteratorHelper(changes);
-	              _context.prev = 3;
+	              _context.prev = 2;
 	              _iterator.s();
-	            case 5:
+	            case 4:
 	              if ((_step = _iterator.n()).done) {
-	                _context.next = 33;
+	                _context.next = 11;
 	                break;
 	              }
 	              change = _step.value;
-	              assemblyName = change.assemblyName, fileId = change.fileId;
+	              assemblyName = change.assemblyName, fileIds = change.fileIds;
+	              _context.next = 9;
+	              return 'gzi' in fileIds ? this.executeOnServerIndexed(backend, assemblyName, fileIds) : this.executeOnServerFasta(backend, assemblyName, fileIds.fa);
+	            case 9:
+	              _context.next = 4;
+	              break;
+	            case 11:
+	              _context.next = 16;
+	              break;
+	            case 13:
+	              _context.prev = 13;
+	              _context.t0 = _context["catch"](2);
+	              _iterator.e(_context.t0);
+	            case 16:
+	              _context.prev = 16;
+	              _iterator.f();
+	              return _context.finish(16);
+	            case 19:
+	            case "end":
+	              return _context.stop();
+	          }
+	        }, _callee, this, [[2, 13, 16, 19]]);
+	      }));
+	      function executeOnServer(_x) {
+	        return _executeOnServer.apply(this, arguments);
+	      }
+	      return executeOnServer;
+	    }()
+	  }, {
+	    key: "executeOnServerIndexed",
+	    value: function () {
+	      var _executeOnServerIndexed = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee2(backend, assemblyName, fileIds) {
+	        var _this$logger$debug, _this$logger;
+	        var CHUNK_SIZE, customChunkSize, FILE_UPLOAD_FOLDER, fa, fai, gzi, assemblyModel, fileModel, filesService, refSeqModel, user, faDoc, faChecksum, faiDoc, faiChecksum, gziDoc, gziChecksum, sequenceAdapter, allSequenceSizes, assemblyDoc, _yield$assemblyModel$, _yield$assemblyModel$2, newAssemblyDoc, sequenceName, _this$logger$debug2, _this$logger2, _yield$refSeqModel$cr, _yield$refSeqModel$cr2, newRefSeqDoc;
+	        return _regeneratorRuntime().wrap(function _callee2$(_context2) {
+	          while (1) switch (_context2.prev = _context2.next) {
+	            case 0:
+	              CHUNK_SIZE = process.env.CHUNK_SIZE;
+	              customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE);
 	              FILE_UPLOAD_FOLDER = process.env.FILE_UPLOAD_FOLDER;
 	              if (FILE_UPLOAD_FOLDER) {
-	                _context.next = 11;
+	                _context2.next = 5;
 	                break;
 	              }
 	              throw new Error('No FILE_UPLOAD_FOLDER found in .env file');
-	            case 11:
-	              _context.next = 13;
-	              return fileModel.findById(fileId).exec();
+	            case 5:
+	              fa = fileIds.fa, fai = fileIds.fai, gzi = fileIds.gzi;
+	              assemblyModel = backend.assemblyModel, fileModel = backend.fileModel, filesService = backend.filesService, refSeqModel = backend.refSeqModel, user = backend.user;
+	              _context2.next = 9;
+	              return fileModel.findById(fa);
+	            case 9:
+	              faDoc = _context2.sent;
+	              faChecksum = faDoc === null || faDoc === void 0 ? void 0 : faDoc.checksum;
+	              if (faChecksum) {
+	                _context2.next = 13;
+	                break;
+	              }
+	              throw new Error("No checksum for file document ".concat(faDoc));
 	            case 13:
-	              fileDoc = _context.sent;
+	              _context2.next = 15;
+	              return fileModel.findById(fai);
+	            case 15:
+	              faiDoc = _context2.sent;
+	              faiChecksum = faiDoc === null || faiDoc === void 0 ? void 0 : faiDoc.checksum;
+	              if (faiChecksum) {
+	                _context2.next = 19;
+	                break;
+	              }
+	              throw new Error("No checksum for file document ".concat(faiDoc));
+	            case 19:
+	              _context2.next = 21;
+	              return fileModel.findById(gzi);
+	            case 21:
+	              gziDoc = _context2.sent;
+	              gziChecksum = gziDoc === null || gziDoc === void 0 ? void 0 : gziDoc.checksum;
+	              if (gziChecksum) {
+	                _context2.next = 25;
+	                break;
+	              }
+	              throw new Error("No checksum for file document ".concat(gziDoc));
+	            case 25:
+	              sequenceAdapter = new indexedfasta_1.BgzipIndexedFasta({
+	                fasta: filesService.getFileHandle(faDoc),
+	                fai: filesService.getFileHandle(faiDoc),
+	                gzi: filesService.getFileHandle(gziDoc)
+	              });
+	              _context2.next = 28;
+	              return sequenceAdapter.getSequenceSizes();
+	            case 28:
+	              allSequenceSizes = _context2.sent;
+	              _context2.next = 31;
+	              return assemblyModel.findOne({
+	                name: assemblyName
+	              }).exec();
+	            case 31:
+	              assemblyDoc = _context2.sent;
+	              if (!assemblyDoc) {
+	                _context2.next = 34;
+	                break;
+	              }
+	              throw new Error("Assembly \"".concat(assemblyName, "\" already exists"));
+	            case 34:
+	              _context2.next = 36;
+	              return assemblyModel.create([{
+	                _id: this.assembly,
+	                name: assemblyName,
+	                user: user,
+	                status: -1,
+	                fileIds: fileIds
+	              }]);
+	            case 36:
+	              _yield$assemblyModel$ = _context2.sent;
+	              _yield$assemblyModel$2 = _slicedToArray(_yield$assemblyModel$, 1);
+	              newAssemblyDoc = _yield$assemblyModel$2[0];
+	              (_this$logger$debug = (_this$logger = this.logger).debug) === null || _this$logger$debug === void 0 || _this$logger$debug.call(_this$logger, "Added new assembly \"".concat(assemblyName, "\", docId \"").concat(newAssemblyDoc._id, "\""));
+	              _context2.t0 = _regeneratorRuntime().keys(allSequenceSizes);
+	            case 41:
+	              if ((_context2.t1 = _context2.t0()).done) {
+	                _context2.next = 51;
+	                break;
+	              }
+	              sequenceName = _context2.t1.value;
+	              _context2.next = 45;
+	              return refSeqModel.create([_objectSpread2(_objectSpread2({
+	                name: sequenceName,
+	                assembly: newAssemblyDoc._id,
+	                length: allSequenceSizes[sequenceName]
+	              }, customChunkSize ? {
+	                chunkSize: customChunkSize
+	              } : null), {}, {
+	                user: user,
+	                status: -1
+	              })]);
+	            case 45:
+	              _yield$refSeqModel$cr = _context2.sent;
+	              _yield$refSeqModel$cr2 = _slicedToArray(_yield$refSeqModel$cr, 1);
+	              newRefSeqDoc = _yield$refSeqModel$cr2[0];
+	              (_this$logger$debug2 = (_this$logger2 = this.logger).debug) === null || _this$logger$debug2 === void 0 || _this$logger$debug2.call(_this$logger2, "Added new refSeq \"".concat(sequenceName, "\", docId \"").concat(newRefSeqDoc._id, "\""));
+	              _context2.next = 41;
+	              break;
+	            case 51:
+	            case "end":
+	              return _context2.stop();
+	          }
+	        }, _callee2, this);
+	      }));
+	      function executeOnServerIndexed(_x2, _x3, _x4) {
+	        return _executeOnServerIndexed.apply(this, arguments);
+	      }
+	      return executeOnServerIndexed;
+	    }()
+	  }, {
+	    key: "executeOnServerFasta",
+	    value: function () {
+	      var _executeOnServerFasta = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee3(backend, assemblyName, fileId) {
+	        var _this$logger$debug3, _this$logger3, _this$logger$debug4, _this$logger4, _this$logger$debug5, _this$logger5;
+	        var assemblyModel, fileModel, user, fileDoc, assemblyDoc, _yield$assemblyModel$3, _yield$assemblyModel$4, newAssemblyDoc;
+	        return _regeneratorRuntime().wrap(function _callee3$(_context3) {
+	          while (1) switch (_context3.prev = _context3.next) {
+	            case 0:
+	              assemblyModel = backend.assemblyModel, fileModel = backend.fileModel, user = backend.user; // Get file checksum
+	              _context3.next = 3;
+	              return fileModel.findById(fileId).exec();
+	            case 3:
+	              fileDoc = _context3.sent;
 	              if (fileDoc) {
-	                _context.next = 16;
+	                _context3.next = 6;
 	                break;
 	              }
 	              throw new Error("File \"".concat(fileId, "\" not found in Mongo"));
-	            case 16:
-	              (_logger$debug = logger.debug) === null || _logger$debug === void 0 || _logger$debug.call(logger, "FileId \"".concat(fileId, "\", checksum \"").concat(fileDoc.checksum, "\""));
+	            case 6:
+	              (_this$logger$debug3 = (_this$logger3 = this.logger).debug) === null || _this$logger$debug3 === void 0 || _this$logger$debug3.call(_this$logger3, "FileId \"".concat(fileId, "\", checksum \"").concat(fileDoc.checksum, "\""));
 	              // Check and add new assembly
-	              _context.next = 19;
+	              _context3.next = 9;
 	              return assemblyModel.findOne({
 	                name: assemblyName
 	              }).exec();
-	            case 19:
-	              assemblyDoc = _context.sent;
+	            case 9:
+	              assemblyDoc = _context3.sent;
 	              if (!assemblyDoc) {
-	                _context.next = 22;
+	                _context3.next = 12;
 	                break;
 	              }
 	              throw new Error("Assembly \"".concat(assemblyName, "\" already exists"));
-	            case 22:
-	              _context.next = 24;
+	            case 12:
+	              _context3.next = 14;
 	              return assemblyModel.create([{
-	                _id: assembly,
+	                _id: this.assembly,
 	                name: assemblyName,
 	                user: user,
-	                status: -1
+	                status: -1,
+	                fileIds: {
+	                  fa: fileId
+	                }
 	              }]);
-	            case 24:
-	              _yield$assemblyModel$ = _context.sent;
-	              _yield$assemblyModel$2 = _slicedToArray(_yield$assemblyModel$, 1);
-	              newAssemblyDoc = _yield$assemblyModel$2[0];
-	              (_logger$debug2 = logger.debug) === null || _logger$debug2 === void 0 || _logger$debug2.call(logger, "Added new assembly \"".concat(assemblyName, "\", docId \"").concat(newAssemblyDoc._id, "\""));
-	              (_logger$debug3 = logger.debug) === null || _logger$debug3 === void 0 || _logger$debug3.call(logger, "File type: \"".concat(fileDoc.type, "\", assemblyId: \"").concat(newAssemblyDoc._id, "\""));
+	            case 14:
+	              _yield$assemblyModel$3 = _context3.sent;
+	              _yield$assemblyModel$4 = _slicedToArray(_yield$assemblyModel$3, 1);
+	              newAssemblyDoc = _yield$assemblyModel$4[0];
+	              (_this$logger$debug4 = (_this$logger4 = this.logger).debug) === null || _this$logger$debug4 === void 0 || _this$logger$debug4.call(_this$logger4, "Added new assembly \"".concat(assemblyName, "\", docId \"").concat(newAssemblyDoc._id, "\""));
+	              (_this$logger$debug5 = (_this$logger5 = this.logger).debug) === null || _this$logger$debug5 === void 0 || _this$logger$debug5.call(_this$logger5, "File type: \"".concat(fileDoc.type, "\", assemblyId: \"").concat(newAssemblyDoc._id, "\""));
 	              // Add refSeqs
 	              // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-	              _context.next = 31;
+	              _context3.next = 21;
 	              return this.addRefSeqIntoDb(fileDoc, newAssemblyDoc._id.toString(), backend);
-	            case 31:
-	              _context.next = 5;
-	              break;
-	            case 33:
-	              _context.next = 38;
-	              break;
-	            case 35:
-	              _context.prev = 35;
-	              _context.t0 = _context["catch"](3);
-	              _iterator.e(_context.t0);
-	            case 38:
-	              _context.prev = 38;
-	              _iterator.f();
-	              return _context.finish(38);
-	            case 41:
+	            case 21:
 	            case "end":
-	              return _context.stop();
+	              return _context3.stop();
 	          }
-	        }, _callee, this, [[3, 35, 38, 41]]);
+	        }, _callee3, this);
 	      }));
-	      function executeOnServer(_x) {
-	        return _executeOnServer.apply(this, arguments);
+	      function executeOnServerFasta(_x5, _x6, _x7) {
+	        return _executeOnServerFasta.apply(this, arguments);
 	      }
-	      return executeOnServer;
+	      return executeOnServerFasta;
 	    }()
 	  }, {
 	    key: "executeOnLocalGFF3",
 	    value: function () {
-	      var _executeOnLocalGFF = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee2(_backend) {
-	        return _regeneratorRuntime().wrap(function _callee2$(_context2) {
-	          while (1) switch (_context2.prev = _context2.next) {
+	      var _executeOnLocalGFF = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee4(_backend) {
+	        return _regeneratorRuntime().wrap(function _callee4$(_context4) {
+	          while (1) switch (_context4.prev = _context4.next) {
 	            case 0:
 	              throw new Error('executeOnLocalGFF3 not implemented');
 	            case 1:
 	            case "end":
-	              return _context2.stop();
+	              return _context4.stop();
 	          }
-	        }, _callee2);
+	        }, _callee4);
 	      }));
-	      function executeOnLocalGFF3(_x2) {
+	      function executeOnLocalGFF3(_x8) {
 	        return _executeOnLocalGFF.apply(this, arguments);
 	      }
 	      return executeOnLocalGFF3;
@@ -15574,16 +15719,16 @@
 	  }, {
 	    key: "executeOnClient",
 	    value: function () {
-	      var _executeOnClient = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee3(_dataStore) {
-	        return _regeneratorRuntime().wrap(function _callee3$(_context3) {
-	          while (1) switch (_context3.prev = _context3.next) {
+	      var _executeOnClient = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee5(_dataStore) {
+	        return _regeneratorRuntime().wrap(function _callee5$(_context5) {
+	          while (1) switch (_context5.prev = _context5.next) {
 	            case 0:
 	            case "end":
-	              return _context3.stop();
+	              return _context5.stop();
 	          }
-	        }, _callee3);
+	        }, _callee5);
 	      }));
-	      function executeOnClient(_x3) {
+	      function executeOnClient(_x9) {
 	        return _executeOnClient.apply(this, arguments);
 	      }
 	      return executeOnClient;
@@ -16536,7 +16681,7 @@
 	});
 	AddRefSeqAliasesChange$1.AddRefSeqAliasesChange = void 0;
 	var common_1$c = dist$1;
-	var util_1$1 = require$$1__default$1["default"];
+	var util_1$2 = require$$1__default$1["default"];
 	var AddRefSeqAliasesChange = /*#__PURE__*/function (_common_1$AssemblySpe) {
 	  _inherits(AddRefSeqAliasesChange, _common_1$AssemblySpe);
 	  var _super = /*#__PURE__*/_createSuper(AddRefSeqAliasesChange);
@@ -16552,7 +16697,7 @@
 	  _createClass(AddRefSeqAliasesChange, [{
 	    key: "executeOnClient",
 	    value: function executeOnClient(clientDataStore) {
-	      var _ref = (0, util_1$1.getSession)(clientDataStore),
+	      var _ref = (0, util_1$2.getSession)(clientDataStore),
 	        assemblyManager = _ref.assemblyManager;
 	      var assembly = assemblyManager.get(this.assembly);
 	      if (!assembly) {
@@ -16691,7 +16836,7 @@
 	/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 	/* eslint-disable @typescript-eslint/no-unsafe-call */
 	var common_1$b = dist$1;
-	var util_1 = require$$1__default$1["default"];
+	var util_1$1 = require$$1__default$1["default"];
 	var DeleteAssemblyChange = /*#__PURE__*/function (_common_1$AssemblySpe) {
 	  _inherits(DeleteAssemblyChange, _common_1$AssemblySpe);
 	  var _super = /*#__PURE__*/_createSuper(DeleteAssemblyChange);
@@ -16822,7 +16967,7 @@
 	              }
 	              throw new Error('No data store');
 	            case 3:
-	              session = (0, util_1.getSession)(dataStore); // If assemblyId is not present in client data store
+	              session = (0, util_1$1.getSession)(dataStore); // If assemblyId is not present in client data store
 	              if (dataStore.assemblies.has(assembly)) {
 	                dataStore.deleteAssembly(assembly);
 	              }
@@ -18835,7 +18980,7 @@
 	    value: true
 	  });
 	  exports.changes = void 0;
-	  var tslib_1 = require$$0;
+	  var tslib_1 = require$$0$1;
 	  var AddAssemblyAndFeaturesFromFileChange_1 = AddAssemblyAndFeaturesFromFileChange$1;
 	  var AddAssemblyFromExternalChange_1 = AddAssemblyFromExternalChange$1;
 	  var AddAssemblyFromFileChange_1 = AddAssemblyFromFileChange$1;
@@ -19038,7 +19183,7 @@
 	    value: true
 	  });
 	  exports.operations = void 0;
-	  var tslib_1 = require$$0;
+	  var tslib_1 = require$$0$1;
 	  var GetAssembliesOperation_1 = GetAssembliesOperation$1;
 	  var GetFeaturesOperation_1 = GetFeaturesOperation$1;
 	  exports.operations = {
@@ -19514,8 +19659,8 @@
 	});
 	CoreValidation$1.CoreValidation = void 0;
 	CoreValidation$1.isTypeChange = isTypeChange;
-	var tslib_1$1 = require$$0;
-	var soSequenceTypes_1 = /*#__PURE__*/tslib_1$1.__importDefault(soSequenceTypes$1);
+	var tslib_1$2 = require$$0$1;
+	var soSequenceTypes_1 = /*#__PURE__*/tslib_1$2.__importDefault(soSequenceTypes$1);
 	var Validation_1$1 = Validation$1;
 	function isTypeChange(thing) {
 	  return 'oldType' in thing && 'newType' in thing;
@@ -19813,7 +19958,7 @@
 	  Object.defineProperty(exports, "__esModule", {
 	    value: true
 	  });
-	  var tslib_1 = require$$0;
+	  var tslib_1 = require$$0$1;
 	  tslib_1.__exportStar(Validation$1, exports);
 	  tslib_1.__exportStar(ValidationSet$1, exports);
 	  tslib_1.__exportStar(CoreValidation$1, exports);
@@ -19886,8 +20031,8 @@
 	});
 	jwtPayload.makeUserSessionId = makeUserSessionId;
 	jwtPayload.getDecodedToken = getDecodedToken;
-	var tslib_1 = require$$0;
-	var jwt_decode_1 = /*#__PURE__*/tslib_1.__importDefault(require$$1);
+	var tslib_1$1 = require$$0$1;
+	var jwt_decode_1 = /*#__PURE__*/tslib_1$1.__importDefault(require$$1);
 	function makeUserSessionId(userOrToken) {
 	  var user = typeof userOrToken === 'string' ? (0, jwt_decode_1["default"])(userOrToken) : userOrToken;
 	  return "".concat(user.id, "-").concat(user.iat);
@@ -19901,7 +20046,7 @@
 	  Object.defineProperty(exports, "__esModule", {
 	    value: true
 	  });
-	  var tslib_1 = require$$0;
+	  var tslib_1 = require$$0$1;
 	  tslib_1.__exportStar(jwtPayload, exports);
 	})(Common);
 
@@ -19913,218 +20058,302 @@
 	  value: true
 	});
 	CDSCheck$1.CDSCheck = void 0;
+	var tslib_1 = require$$0$1;
 	var common_1 = dist$1;
-	// import ObjectID from 'bson-objectid'
-	// enum STOP_CODONS {
-	//   'TAG',
-	//   'TAA',
-	//   'TGA',
-	// }
-	// const iupacComplements: Record<string, string | undefined> = {
-	//   G: 'C',
-	//   A: 'T',
-	//   T: 'A',
-	//   C: 'G',
-	//   R /* G or A */: 'Y',
-	//   Y /* T or C */: 'R',
-	//   M /* A or C */: 'K',
-	//   K /* G or T */: 'M',
-	//   S /* G or C */: 'S',
-	//   W /* A or T */: 'W',
-	//   H /* A or C or T */: 'D',
-	//   B /* G or T or C */: 'V',
-	//   V /* G or C or A */: 'B',
-	//   D /* G or A or T */: 'H',
-	//   N /* G or A or T or C */: 'N',
-	// }
-	// function reverseComplement(dna: string): string {
-	//   const complement: string[] = []
-	//   for (const nt of dna) {
-	//     const rc = iupacComplements[nt.toUpperCase()]
-	//     if (rc === undefined) {
-	//       throw new TypeError(`Cannot complement nucleotide: "${nt}"`)
-	//     }
-	//     if (nt === nt.toLowerCase()) {
-	//       complement.push(rc.toLowerCase())
-	//     } else {
-	//       complement.push(rc)
-	//     }
-	//   }
-	//   return complement.reverse().join('')
-	// }
-	// async function getSequenceFromSingleFeature(
-	//   feature: AnnotationFeatureSnapshot,
-	//   getSequence: (start: number, end: number) => Promise<string>,
-	// ) {
-	//   let seq = ''
-	//   if (
-	//     feature.discontinuousLocations !== undefined &&
-	//     feature.discontinuousLocations.length > 0
-	//   ) {
-	//     for (const loc of feature.discontinuousLocations) {
-	//       seq = seq + (await getSequence(loc.start, loc.end))
-	//     }
-	//   } else {
-	//     seq = await getSequence(feature.start, feature.end)
-	//   }
-	//   if (feature.strand === -1) {
-	//     return reverseComplement(seq)
-	//   }
-	//   return seq
-	// }
-	// async function getSequenceFromMultipleFeatures(
-	//   features: AnnotationFeatureSnapshot[],
-	//   getSequence: (start: number, end: number) => Promise<string>,
-	// ) {
-	//   const strands = features.map((feature) => feature.strand)
-	//   if (!strands.every((strand) => strand === strands[0])) {
-	//     throw new Error(
-	//       `Strands do not match in features: "${features
-	//         .map((f) => f._id)
-	//         .join(', ')}"`,
-	//     )
-	//   }
-	//   let seq = ''
-	//   for (const feature of features) {
-	//     seq = seq + (await getSequence(feature.start, feature.end))
-	//   }
-	//   if (strands[0] === -1) {
-	//     return reverseComplement(seq)
-	//   }
-	//   return seq
-	// }
-	// function splitSequenceInCodons(cds: string): string[] {
-	//   const codons: string[] = []
-	//   for (let i = 0; i <= cds.length - 3; i += 3) {
-	//     codons.push(cds.slice(i, i + 3))
-	//   }
-	//   return codons
-	// }
-	// function getOriginalCodonLocation(
-	//   feature: AnnotationFeatureSnapshot | AnnotationFeatureSnapshot[],
-	//   index: number,
-	// ): [number, number] {
-	//   let lengthToStart = index * 3
-	//   let lengthToEnd = lengthToStart + 3
-	//   if (Array.isArray(feature)) {
-	//     let startLocation: number | undefined = undefined,
-	//       endLocation: number | undefined = undefined
-	//     for (const f of feature) {
-	//       const featureLength = f.end - f.start
-	//       if (startLocation === undefined && featureLength > lengthToStart) {
-	//         startLocation = f.start + lengthToStart
-	//       } else {
-	//         lengthToStart -= featureLength
-	//       }
-	//       if (endLocation === undefined && featureLength > lengthToEnd) {
-	//         endLocation = f.start + lengthToEnd
-	//       } else {
-	//         lengthToEnd -= featureLength
-	//       }
-	//       if (startLocation !== undefined && endLocation !== undefined) {
-	//         return [startLocation, endLocation]
-	//       }
-	//     }
-	//     throw new Error('Could not determine original CDS location')
-	//   } else {
-	//     if (
-	//       feature.discontinuousLocations !== undefined &&
-	//       feature.discontinuousLocations.length > 0
-	//     ) {
-	//       let startLocation: number | undefined = undefined,
-	//         endLocation: number | undefined = undefined
-	//       for (const loc of feature.discontinuousLocations) {
-	//         const locLength = loc.end - loc.start
-	//         if (startLocation === undefined && locLength > lengthToStart) {
-	//           startLocation = loc.start + lengthToStart
-	//         } else {
-	//           lengthToStart -= locLength
-	//         }
-	//         if (endLocation === undefined && locLength > lengthToEnd) {
-	//           endLocation = loc.start + lengthToEnd
-	//         } else {
-	//           lengthToEnd -= locLength
-	//         }
-	//         if (startLocation !== undefined && endLocation !== undefined) {
-	//           return [startLocation, endLocation]
-	//         }
-	//       }
-	//       throw new Error('Could not determine original CDS location')
-	//     } else {
-	//       return [feature.start + lengthToStart, feature.start + lengthToEnd]
-	//     }
-	//   }
-	// }
-	// async function checkCDS(
-	//   feature: AnnotationFeatureSnapshot | AnnotationFeatureSnapshot[],
-	//   getSequence: (start: number, end: number) => Promise<string>,
-	// ): Promise<CheckResultSnapshot[]> {
-	//   const checkResults: CheckResultSnapshot[] = []
-	//   let _id: string,
-	//     ids: string[],
-	//     start: number,
-	//     end: number,
-	//     refSeq: string,
-	//     sequence: string
-	//   if (Array.isArray(feature)) {
-	//     sequence = await getSequenceFromMultipleFeatures(feature, getSequence)
-	//     ids = feature.map((f) => f._id)
-	//     _id = ids.join(',')
-	//     ;[{ refSeq, start }] = feature
-	//     const lastFeature = feature.at(-1)
-	//     if (!lastFeature) {
-	//       throw new Error('Zero-length feature array encountered')
-	//     }
-	//     ;({ end } = lastFeature)
-	//   } else {
-	//     sequence = await getSequenceFromSingleFeature(feature, getSequence)
-	//     ;({ _id, end, refSeq, start } = feature)
-	//     ids = [_id]
-	//   }
-	//   const codons = splitSequenceInCodons(sequence)
-	//   if (sequence.length % 3 === 0) {
-	//     const lastCodon = codons.pop() // Last codon is supposed to be a stop
-	//     if (!lastCodon) {
-	//       throw new Error(`No sequence found for feature "${_id}"`)
-	//     }
-	//     if (!(lastCodon.toUpperCase() in STOP_CODONS)) {
-	//       checkResults.push({
-	//         _id: new ObjectID().toHexString(),
-	//         name: 'MissingStopCodonCheck',
-	//         ids,
-	//         refSeq: refSeq.toString(),
-	//         start: end,
-	//         end,
-	//         message: `Feature "${_id}" is missing a stop codon`,
-	//       })
-	//     }
-	//   } else {
-	//     checkResults.push({
-	//       _id: new ObjectID().toHexString(),
-	//       name: 'MultipleOfThreeCheck',
-	//       ids,
-	//       refSeq: refSeq.toString(),
-	//       start,
-	//       end,
-	//       message: `The coding sequence for feature "${_id}" is not a multiple of three`,
-	//     })
-	//   }
-	//   for (const [idx, codon] of codons.entries()) {
-	//     const [codonStart, codonEnd] = getOriginalCodonLocation(feature, idx)
-	//     if (codon.toUpperCase() in STOP_CODONS) {
-	//       checkResults.push({
-	//         _id: new ObjectID().toHexString(),
-	//         name: 'InternalStopCodonCheck',
-	//         ids,
-	//         refSeq: refSeq.toString(),
-	//         start: codonStart,
-	//         end: codonEnd,
-	//         message: `The coding sequence for feature "${_id}" has an internal stop codon`,
-	//       })
-	//     }
-	//   }
-	//   return checkResults
-	// }
+	var util_1 = require$$1__default$1["default"];
+	var bson_objectid_1 = /*#__PURE__*/tslib_1.__importDefault(objectid);
+	var STOP_CODONS;
+	(function (STOP_CODONS) {
+	  STOP_CODONS[STOP_CODONS["TAG"] = 0] = "TAG";
+	  STOP_CODONS[STOP_CODONS["TAA"] = 1] = "TAA";
+	  STOP_CODONS[STOP_CODONS["TGA"] = 2] = "TGA";
+	})(STOP_CODONS || (STOP_CODONS = {}));
+	var iupacComplements = {
+	  G: 'C',
+	  A: 'T',
+	  T: 'A',
+	  C: 'G',
+	  R /* G or A */: 'Y',
+	  Y /* T or C */: 'R',
+	  M /* A or C */: 'K',
+	  K /* G or T */: 'M',
+	  S /* G or C */: 'S',
+	  W /* A or T */: 'W',
+	  H /* A or C or T */: 'D',
+	  B /* G or T or C */: 'V',
+	  V /* G or C or A */: 'B',
+	  D /* G or A or T */: 'H',
+	  N /* G or A or T or C */: 'N'
+	};
+	function reverseComplement(dna) {
+	  var complement = [];
+	  var _iterator = _createForOfIteratorHelper(dna),
+	    _step;
+	  try {
+	    for (_iterator.s(); !(_step = _iterator.n()).done;) {
+	      var nt = _step.value;
+	      var rc = iupacComplements[nt.toUpperCase()];
+	      if (rc === undefined) {
+	        throw new TypeError("Cannot complement nucleotide: \"".concat(nt, "\""));
+	      }
+	      if (nt === nt.toLowerCase()) {
+	        complement.push(rc.toLowerCase());
+	      } else {
+	        complement.push(rc);
+	      }
+	    }
+	  } catch (err) {
+	    _iterator.e(err);
+	  } finally {
+	    _iterator.f();
+	  }
+	  return complement.reverse().join('');
+	}
+	function getCDSSequence(_x, _x2, _x3) {
+	  return _getCDSSequence.apply(this, arguments);
+	}
+	function _getCDSSequence() {
+	  _getCDSSequence = _asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee2(cdsLocation, strand, getSequence) {
+	    var sequences;
+	    return _regeneratorRuntime().wrap(function _callee2$(_context2) {
+	      while (1) switch (_context2.prev = _context2.next) {
+	        case 0:
+	          _context2.next = 2;
+	          return Promise.all(cdsLocation.map(function (_ref5) {
+	            var max = _ref5.max,
+	              min = _ref5.min;
+	            return getSequence(min, max);
+	          }));
+	        case 2:
+	          sequences = _context2.sent;
+	          if (!(strand === -1)) {
+	            _context2.next = 5;
+	            break;
+	          }
+	          return _context2.abrupt("return", sequences.map(function (seq) {
+	            return reverseComplement(seq);
+	          }).join(''));
+	        case 5:
+	          return _context2.abrupt("return", sequences.join(''));
+	        case 6:
+	        case "end":
+	          return _context2.stop();
+	      }
+	    }, _callee2);
+	  }));
+	  return _getCDSSequence.apply(this, arguments);
+	}
+	function splitSequenceInCodons(cds) {
+	  var codons = [];
+	  for (var i = 0; i <= cds.length - 3; i += 3) {
+	    codons.push(cds.slice(i, i + 3));
+	  }
+	  return codons;
+	}
+	function getOriginalCodonLocation(cdsLocation, strand, index) {
+	  var lengthToStart = index * 3;
+	  var lengthToEnd = lengthToStart + 3;
+	  var startLocation = undefined,
+	    endLocation = undefined;
+	  var _iterator2 = _createForOfIteratorHelper(cdsLocation),
+	    _step2;
+	  try {
+	    for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
+	      var loc = _step2.value;
+	      var locLength = loc.max - loc.min;
+	      if (startLocation === undefined && locLength > lengthToStart) {
+	        startLocation = loc.min + lengthToStart;
+	      } else {
+	        lengthToStart -= locLength;
+	      }
+	      if (endLocation === undefined && locLength > lengthToEnd) {
+	        endLocation = loc.min + lengthToEnd;
+	      } else {
+	        lengthToEnd -= locLength;
+	      }
+	      if (startLocation !== undefined && endLocation !== undefined) {
+	        return [startLocation, endLocation];
+	      }
+	    }
+	  } catch (err) {
+	    _iterator2.e(err);
+	  } finally {
+	    _iterator2.f();
+	  }
+	  return;
+	}
+	function checkMRNA(_x4, _x5) {
+	  return _checkMRNA.apply(this, arguments);
+	}
+	function _checkMRNA() {
+	  _checkMRNA = _asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee3(feature, getSequence) {
+	    var checkResults, _id, max, min, refSeq, strand, cdsLocations, ids, _iterator4, _step4, cdsLocation, sequence, codons, lastCodon, _iterator5, _step5, _step5$value, idx, codon, location, _location, codonStart, codonEnd;
+	    return _regeneratorRuntime().wrap(function _callee3$(_context3) {
+	      while (1) switch (_context3.prev = _context3.next) {
+	        case 0:
+	          checkResults = [];
+	          _id = feature._id, max = feature.max, min = feature.min, refSeq = feature.refSeq, strand = feature.strand;
+	          cdsLocations = getCDSLocations(feature);
+	          if (cdsLocations) {
+	            _context3.next = 5;
+	            break;
+	          }
+	          return _context3.abrupt("return", checkResults);
+	        case 5:
+	          ids = [_id];
+	          _iterator4 = _createForOfIteratorHelper(cdsLocations);
+	          _context3.prev = 7;
+	          _iterator4.s();
+	        case 9:
+	          if ((_step4 = _iterator4.n()).done) {
+	            _context3.next = 20;
+	            break;
+	          }
+	          cdsLocation = _step4.value;
+	          _context3.next = 13;
+	          return getCDSSequence(cdsLocation, strand, getSequence);
+	        case 13:
+	          sequence = _context3.sent;
+	          codons = splitSequenceInCodons(sequence);
+	          if (sequence.length % 3 === 0) {
+	            lastCodon = codons.pop(); // Last codon is supposed to be a stop
+	            if (lastCodon && !(lastCodon.toUpperCase() in STOP_CODONS)) {
+	              checkResults.push({
+	                _id: new bson_objectid_1["default"]().toHexString(),
+	                name: 'MissingStopCodonCheck',
+	                ids: ids,
+	                refSeq: refSeq.toString(),
+	                start: max,
+	                end: max,
+	                message: "Feature \"".concat(_id, "\" is missing a stop codon")
+	              });
+	            }
+	          } else {
+	            checkResults.push({
+	              _id: new bson_objectid_1["default"]().toHexString(),
+	              name: 'MultipleOfThreeCheck',
+	              ids: ids,
+	              refSeq: refSeq.toString(),
+	              start: min,
+	              end: max,
+	              message: "The coding sequence for feature \"".concat(_id, "\" is not a multiple of three")
+	            });
+	          }
+	          _iterator5 = _createForOfIteratorHelper(codons.entries());
+	          try {
+	            for (_iterator5.s(); !(_step5 = _iterator5.n()).done;) {
+	              _step5$value = _slicedToArray(_step5.value, 2), idx = _step5$value[0], codon = _step5$value[1];
+	              location = getOriginalCodonLocation(cdsLocation, strand, idx);
+	              if (location && codon.toUpperCase() in STOP_CODONS) {
+	                _location = _slicedToArray(location, 2), codonStart = _location[0], codonEnd = _location[1];
+	                checkResults.push({
+	                  _id: new bson_objectid_1["default"]().toHexString(),
+	                  name: 'InternalStopCodonCheck',
+	                  ids: ids,
+	                  refSeq: refSeq.toString(),
+	                  start: codonStart,
+	                  end: codonEnd,
+	                  message: "The coding sequence for feature \"".concat(_id, "\" has an internal stop codon")
+	                });
+	              }
+	            }
+	          } catch (err) {
+	            _iterator5.e(err);
+	          } finally {
+	            _iterator5.f();
+	          }
+	        case 18:
+	          _context3.next = 9;
+	          break;
+	        case 20:
+	          _context3.next = 25;
+	          break;
+	        case 22:
+	          _context3.prev = 22;
+	          _context3.t0 = _context3["catch"](7);
+	          _iterator4.e(_context3.t0);
+	        case 25:
+	          _context3.prev = 25;
+	          _iterator4.f();
+	          return _context3.finish(25);
+	        case 28:
+	          return _context3.abrupt("return", checkResults);
+	        case 29:
+	        case "end":
+	          return _context3.stop();
+	      }
+	    }, _callee3, null, [[7, 22, 25, 28]]);
+	  }));
+	  return _checkMRNA.apply(this, arguments);
+	}
+	function getCDSLocations(feature) {
+	  if (feature.type !== 'mRNA') {
+	    return;
+	  }
+	  var children = feature.children,
+	    strand = feature.strand;
+	  if (!children) {
+	    return;
+	  }
+	  var cdsChildren = Object.values(children).filter(function (child) {
+	    return child.type === 'CDS';
+	  });
+	  if (cdsChildren.length === 0) {
+	    return;
+	  }
+	  var cdsLocations = [];
+	  var _iterator3 = _createForOfIteratorHelper(cdsChildren),
+	    _step3;
+	  try {
+	    var _loop = function _loop() {
+	      var cds = _step3.value;
+	      var cdsMax = cds.max,
+	        cdsMin = cds.min;
+	      var locs = [];
+	      for (var _i = 0, _Object$values = Object.values(children); _i < _Object$values.length; _i++) {
+	        var child = _Object$values[_i];
+	        if (child.type !== 'exon') {
+	          continue;
+	        }
+	        var _ref = (0, util_1.intersection2)(cdsMin, cdsMax, child.min, child.max),
+	          _ref2 = _slicedToArray(_ref, 2),
+	          start = _ref2[0],
+	          end = _ref2[1];
+	        if (start !== undefined && end !== undefined) {
+	          locs.push({
+	            min: start,
+	            max: end
+	          });
+	        }
+	      }
+	      locs.sort(function (_ref3, _ref4) {
+	        var a = _ref3.min;
+	        var b = _ref4.min;
+	        return a - b;
+	      });
+	      if (strand === -1) {
+	        locs.reverse();
+	      }
+	      var nextPhase = 0;
+	      var phasedLocs = locs.map(function (loc) {
+	        var phase = nextPhase;
+	        nextPhase = (3 - (loc.max - loc.min - phase + 3) % 3) % 3;
+	        return _objectSpread2(_objectSpread2({}, loc), {}, {
+	          phase: phase
+	        });
+	      });
+	      cdsLocations.push(phasedLocs);
+	    };
+	    for (_iterator3.s(); !(_step3 = _iterator3.n()).done;) {
+	      _loop();
+	    }
+	  } catch (err) {
+	    _iterator3.e(err);
+	  } finally {
+	    _iterator3.f();
+	  }
+	  return cdsLocations;
+	}
 	var CDSCheck = /*#__PURE__*/function (_common_1$Check) {
 	  _inherits(CDSCheck, _common_1$Check);
 	  var _super = /*#__PURE__*/_createSuper(CDSCheck);
@@ -20143,21 +20372,53 @@
 	  _createClass(CDSCheck, [{
 	    key: "checkFeature",
 	    value: function () {
-	      var _checkFeature = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee(_feature, _getSequence) {
+	      var _checkFeature = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/_regeneratorRuntime().mark(function _callee(feature, getSequence) {
+	        var checkResults, _i2, _Object$values2, child;
 	        return _regeneratorRuntime().wrap(function _callee$(_context) {
 	          while (1) switch (_context.prev = _context.next) {
 	            case 0:
-	              _context.next = 2;
-	              return Promise.resolve();
+	              if (!(feature.type === 'mRNA')) {
+	                _context.next = 2;
+	                break;
+	              }
+	              return _context.abrupt("return", checkMRNA(feature, getSequence));
 	            case 2:
+	              if (feature.children) {
+	                _context.next = 4;
+	                break;
+	              }
 	              return _context.abrupt("return", []);
-	            case 3:
+	            case 4:
+	              checkResults = [];
+	              _i2 = 0, _Object$values2 = Object.values(feature.children);
+	            case 6:
+	              if (!(_i2 < _Object$values2.length)) {
+	                _context.next = 19;
+	                break;
+	              }
+	              child = _Object$values2[_i2];
+	              _context.t0 = checkResults.push;
+	              _context.t1 = checkResults;
+	              _context.t2 = _toConsumableArray;
+	              _context.next = 13;
+	              return this.checkFeature(child, getSequence);
+	            case 13:
+	              _context.t3 = _context.sent;
+	              _context.t4 = (0, _context.t2)(_context.t3);
+	              _context.t0.apply.call(_context.t0, _context.t1, _context.t4);
+	            case 16:
+	              _i2++;
+	              _context.next = 6;
+	              break;
+	            case 19:
+	              return _context.abrupt("return", checkResults);
+	            case 20:
 	            case "end":
 	              return _context.stop();
 	          }
-	        }, _callee);
+	        }, _callee, this);
 	      }));
-	      function checkFeature(_x, _x2) {
+	      function checkFeature(_x6, _x7) {
 	        return _checkFeature.apply(this, arguments);
 	      }
 	      return checkFeature;
@@ -20172,12 +20433,13 @@
 	  Object.defineProperty(exports, "__esModule", {
 	    value: true
 	  });
-	  var tslib_1 = require$$0;
+	  var tslib_1 = require$$0$1;
 	  tslib_1.__exportStar(CDSCheck$1, exports);
 	})(Checks);
 
 	var util$1 = {};
 
+	/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 	Object.defineProperty(util$1, "__esModule", {
 	  value: true
 	});
@@ -20299,7 +20561,7 @@
 	  Object.defineProperty(exports, "__esModule", {
 	    value: true
 	  });
-	  var tslib_1 = require$$0;
+	  var tslib_1 = require$$0$1;
 	  tslib_1.__exportStar(Changes, exports);
 	  tslib_1.__exportStar(Operations, exports);
 	  tslib_1.__exportStar(Validations, exports);
@@ -20352,7 +20614,7 @@
 	}), 'Add');
 	default_1$a = Add["default"] = _default$c;
 
-	var version = "0.1.19";
+	var version = "0.1.20";
 
 	const ApolloConfigSchema = configuration.ConfigurationSchema('ApolloInternetAccount', {
 	    baseURL: {
@@ -27870,7 +28132,7 @@
 	    for (const ref of assembly.refSeqs.values()) {
 	        for (const feature of ref.features.values()) {
 	            for (const check of dist$3.checkRegistry.getChecks().values()) {
-	                const result = await check.checkFeature(require$$1$4.getSnapshot(feature), (start, stop) => Promise.resolve(ref.getSequence(start, stop)));
+	                const result = await check.checkFeature(require$$1$3.getSnapshot(feature), (start, stop) => Promise.resolve(ref.getSequence(start, stop)));
 	                checkResults.push(...result);
 	            }
 	        }
@@ -27891,7 +28153,7 @@
 	}
 	/** given a session, get our ApolloInternetAccount */
 	function getApolloInternetAccount(session) {
-	    const { internetAccounts } = require$$1$4.getParent(session);
+	    const { internetAccounts } = require$$1$3.getParent(session);
 	    return internetAccounts.find((ia) => ia.type === 'ApolloInternetAccount');
 	}
 
@@ -27954,7 +28216,7 @@
 	    FileType["EXTERNAL"] = "text/x-external";
 	})(FileType || (FileType = {}));
 	function AddAssembly({ changeManager, handleClose, session, }) {
-	    const { internetAccounts } = require$$1$4.getRoot(session);
+	    const { internetAccounts } = require$$1$3.getRoot(session);
 	    const { notify } = session;
 	    const apolloInternetAccounts = internetAccounts.filter((ia) => ia.type === 'ApolloInternetAccount');
 	    if (apolloInternetAccounts.length === 0) {
@@ -28089,7 +28351,7 @@
 	            const fileUploadChangeBase = {
 	                assembly: new objectid().toHexString(),
 	                assemblyName,
-	                fileId,
+	                fileIds: { fa: fileId },
 	            };
 	            change =
 	                fileType === FileType.GFF3 && importFeatures
@@ -34867,7 +35129,7 @@
 	async function textSearch(text, tx, signal) {
 	    const db = await this.db;
 	    const myTx = tx ?? db.transaction(['nodes']);
-	    require$$1$3.checkAbortSignal(signal);
+	    require$$1$2.checkAbortSignal(signal);
 	    const queryWords = [...wordsInString(text)];
 	    const queries = [];
 	    /**
@@ -34877,10 +35139,10 @@
 	    const initialMatches = new Map();
 	    // find startsWith and complete matches
 	    queries.push(...queryWords.map(async (queryWord, queryWordIndex) => {
-	        require$$1$3.checkAbortSignal(signal);
+	        require$$1$2.checkAbortSignal(signal);
 	        const idx = myTx.objectStore('nodes').index('full-text-words');
 	        for await (const cursor of idx.iterate(IDBKeyRange.bound(queryWord, `${queryWord}\uFFFF`, false, false))) {
-	            require$$1$3.checkAbortSignal(signal);
+	            require$$1$2.checkAbortSignal(signal);
 	            const term = cursor.value;
 	            const termMatches = initialMatches.get(term.id) ?? [
 	                term,
@@ -34891,11 +35153,11 @@
 	        }
 	    }));
 	    await Promise.all(queries);
-	    require$$1$3.checkAbortSignal(signal);
+	    require$$1$2.checkAbortSignal(signal);
 	    // now rank the term matches and add some detail
 	    const results = [];
 	    for (const [, [term, wordIndexes]] of initialMatches) {
-	        require$$1$3.checkAbortSignal(signal);
+	        require$$1$2.checkAbortSignal(signal);
 	        results.push(...elaborateMatch(this.textIndexFields, term, wordIndexes, queryWords, this.prefixes));
 	    }
 	    // sort the terms by score descending
@@ -35636,7 +35898,7 @@
 	        return errors;
 	    }
 	    get sourceType() {
-	        if (require$$1$3.isUriLocation(this.sourceLocation)) {
+	        if (require$$1$2.isUriLocation(this.sourceLocation)) {
 	            if (this.sourceLocation.uri.endsWith('.json')) {
 	                return 'obo-graph-json';
 	            }
@@ -35871,12 +36133,12 @@
 	    }
 	}
 
-	const OntologyRecordType = require$$1$4.types
+	const OntologyRecordType = require$$1$3.types
 	    .model('OntologyRecord', {
-	    name: require$$1$4.types.string,
+	    name: require$$1$3.types.string,
 	    version: 'unversioned',
-	    source: require$$1$4.types.union(mst.LocalPathLocation, mst.UriLocation, mst.BlobLocation),
-	    options: require$$1$4.types.frozen(),
+	    source: require$$1$3.types.union(mst.LocalPathLocation, mst.UriLocation, mst.BlobLocation),
+	    options: require$$1$3.types.frozen(),
 	})
 	    .volatile((_self) => ({
 	    dataStore: undefined,
@@ -35887,19 +36149,19 @@
 	        return;
 	    },
 	    initDataStore() {
-	        self.dataStore = new OntologyStore(self.name, self.version, require$$1$4.getSnapshot(self.source), self.options);
+	        self.dataStore = new OntologyStore(self.name, self.version, require$$1$3.getSnapshot(self.source), self.options);
 	    },
 	    afterCreate() {
-	        require$$1$4.addDisposer(self, mobx.autorun(() => {
+	        require$$1$3.addDisposer(self, mobx.autorun(() => {
 	            this.initDataStore();
 	        }));
 	    },
 	}));
-	const OntologyManagerType = require$$1$4.types
+	const OntologyManagerType = require$$1$3.types
 	    .model('OntologyManager', {
 	    // create, update, and delete ontologies
-	    ontologies: require$$1$4.types.array(OntologyRecordType),
-	    prefixes: require$$1$4.types.optional(require$$1$4.types.map(require$$1$4.types.string), {
+	    ontologies: require$$1$3.types.array(OntologyRecordType),
+	    prefixes: require$$1$3.types.optional(require$$1$3.types.map(require$$1$3.types.string), {
 	        'GO:': 'http://purl.obolibrary.org/obo/GO_',
 	        'SO:': 'http://purl.obolibrary.org/obo/SO_',
 	    }),
@@ -36039,7 +36301,7 @@
 	                    setCurrentOntologyTerm(term);
 	                }
 	            }, (error) => {
-	                if (!signal.aborted && !require$$1$3.isAbortException(error)) {
+	                if (!signal.aborted && !require$$1$2.isAbortException(error)) {
 	                    setCurrentOntologyTermInvalid(String(error));
 	                }
 	            });
@@ -36058,7 +36320,7 @@
 	                    setTermChoices(soTerms);
 	                }
 	            }, (error) => {
-	                if (!signal.aborted && !require$$1$3.isAbortException(error)) {
+	                if (!signal.aborted && !require$$1$2.isAbortException(error)) {
 	                    session.notify(error.message, 'error');
 	                }
 	            });
@@ -36384,7 +36646,7 @@
 	        }
 	        const featureIds = [];
 	        // Let's add featureId to each child recursively
-	        const newFeatureLine = generateNewIds(require$$1$4.getSnapshot(sourceFeature), featureIds);
+	        const newFeatureLine = generateNewIds(require$$1$3.getSnapshot(sourceFeature), featureIds);
 	        // Clear possible parentId -attribute.
 	        const attributeMap = {
 	            ...newFeatureLine.attributes,
@@ -36472,7 +36734,7 @@
 
 	/* eslint-disable @typescript-eslint/no-misused-promises */
 	function DeleteAssembly({ changeManager, handleClose, session, }) {
-	    const { internetAccounts } = require$$1$4.getRoot(session);
+	    const { internetAccounts } = require$$1$3.getRoot(session);
 	    const [selectedAssembly, setSelectedAssembly] = React.useState();
 	    const [errorMessage, setErrorMessage] = React.useState('');
 	    const [confirmDelete, setconfirmDelete] = React.useState(false);
@@ -36554,7 +36816,7 @@
 	            changedIds: [sourceFeature._id],
 	            typeName: 'DeleteFeatureChange',
 	            assembly: sourceAssemblyId,
-	            deletedFeature: require$$1$4.getSnapshot(sourceFeature),
+	            deletedFeature: require$$1$3.getSnapshot(sourceFeature),
 	            parentFeatureId: sourceFeature.parent?._id,
 	        });
 	        await changeManager.submit(change);
@@ -36744,7 +37006,7 @@
 	                continue;
 	            }
 	            for (const [, feature] of features) {
-	                gff3Items.push(dist$2.makeGFF3Feature(require$$1$4.getSnapshot(feature)));
+	                gff3Items.push(dist$2.makeGFF3Feature(require$$1$3.getSnapshot(feature)));
 	            }
 	        }
 	        for (const sequenceFeature of sequenceFeatures) {
@@ -36934,7 +37196,7 @@
 	}
 
 	function LogOut({ handleClose, session }) {
-	    const { internetAccounts } = require$$1$4.getRoot(session);
+	    const { internetAccounts } = require$$1$3.getRoot(session);
 	    const [errorMessage, setErrorMessage] = React.useState('');
 	    const apolloInternetAccounts = internetAccounts.filter((ia) => ia.type === 'ApolloInternetAccount');
 	    if (apolloInternetAccounts.length === 0) {
@@ -36969,7 +37231,7 @@
 	}
 
 	function ManageChecks({ handleClose, session }) {
-	    const { internetAccounts } = require$$1$4.getRoot(session);
+	    const { internetAccounts } = require$$1$3.getRoot(session);
 	    const [selectedAssembly, setSelectedAssembly] = React.useState();
 	    const [errorMessage, setErrorMessage] = React.useState('');
 	    const [submitted, setSubmitted] = React.useState(false);
@@ -37130,7 +37392,7 @@
 
 	/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 	function ManageUsers({ changeManager, handleClose, session, }) {
-	    const { internetAccounts } = require$$1$4.getRoot(session);
+	    const { internetAccounts } = require$$1$3.getRoot(session);
 	    const apolloInternetAccounts = internetAccounts.filter((ia) => ia.type === 'ApolloInternetAccount' && ia.role?.includes('admin'));
 	    if (apolloInternetAccounts.length === 0) {
 	        throw new Error('No Apollo internet account found');
@@ -37185,7 +37447,26 @@
 	            headerName: 'Role',
 	            width: 140,
 	            type: 'singleSelect',
-	            valueOptions: ['', 'readOnly', 'user', 'admin'],
+	            valueOptions: ['readOnly', 'user', 'admin', 'none'],
+	            getOptionLabel(value) {
+	                switch (value) {
+	                    case 'readOnly': {
+	                        return 'Read-only';
+	                    }
+	                    case 'user': {
+	                        return 'User';
+	                    }
+	                    case 'admin': {
+	                        return 'Admin';
+	                    }
+	                    case 'none': {
+	                        return 'None';
+	                    }
+	                    default: {
+	                        return 'unknown';
+	                    }
+	                }
+	            },
 	            editable: true,
 	        },
 	        {
@@ -37767,7 +38048,7 @@
 	// }
 	// const hiliteRegex = /(?<=<em class="hilite">)(.*?)(?=<\/em>)/g
 	function TermTagWithTooltip({ getTagProps, index, ontology, termId, }) {
-	    const manager = require$$1$4.getParent(ontology, 2);
+	    const manager = require$$1$3.getParent(ontology, 2);
 	    const [description, setDescription] = React__namespace.useState('');
 	    const [errorMessage, setErrorMessage] = React__namespace.useState('');
 	    React__namespace.useEffect(() => {
@@ -37808,7 +38089,7 @@
 	    const [options, setOptions] = React__namespace.useState([]);
 	    const [loading, setLoading] = React__namespace.useState(false);
 	    const [errorMessage, setErrorMessage] = React__namespace.useState('');
-	    const getOntologyTerms = React__namespace.useMemo(() => require$$0$1.debounce(async (request, callback) => {
+	    const getOntologyTerms = React__namespace.useMemo(() => require$$0$2.debounce(async (request, callback) => {
 	        if (!ontology) {
 	            return;
 	        }
@@ -37838,7 +38119,7 @@
 	            callback(options);
 	        }
 	        catch (error) {
-	            if (!require$$1$3.isAbortException(error)) {
+	            if (!require$$1$2.isAbortException(error)) {
 	                setErrorMessage(String(error));
 	            }
 	        }
@@ -37968,7 +38249,7 @@
 	}
 	function ModifyFeatureAttribute({ changeManager, handleClose, session, sourceAssemblyId, sourceFeature, }) {
 	    const { notify } = session;
-	    const { internetAccounts } = require$$1$4.getRoot(session);
+	    const { internetAccounts } = require$$1$3.getRoot(session);
 	    const internetAccount = React.useMemo(() => {
 	        return internetAccounts.find((ia) => ia.type === 'ApolloInternetAccount');
 	    }, [internetAccounts]);
@@ -37979,12 +38260,12 @@
 	        if (key.startsWith('gff_')) {
 	            const newKey = key.slice(4);
 	            const capitalizedKey = newKey.charAt(0).toUpperCase() + newKey.slice(1);
-	            return [capitalizedKey, require$$1$4.getSnapshot(value)];
+	            return [capitalizedKey, require$$1$3.getSnapshot(value)];
 	        }
 	        if (key === '_id') {
-	            return ['ID', require$$1$4.getSnapshot(value)];
+	            return ['ID', require$$1$3.getSnapshot(value)];
 	        }
-	        return [key, require$$1$4.getSnapshot(value)];
+	        return [key, require$$1$3.getSnapshot(value)];
 	    })));
 	    const [showAddNewForm, setShowAddNewForm] = React.useState(false);
 	    const [newAttributeKey, setNewAttributeKey] = React.useState('');
@@ -38237,7 +38518,7 @@
 	                adapter: { type: 'ApolloSequenceAdapter', assemblyId },
 	                metadata: {
 	                    apollo: true,
-	                    ...(require$$1$3.isElectron
+	                    ...(require$$1$2.isElectron
 	                        ? { file: file.path }
 	                        : {}),
 	                },
@@ -38288,7 +38569,7 @@
 	    },
 	}));
 	function ViewChangeLog({ handleClose, session }) {
-	    const { internetAccounts } = require$$1$4.getRoot(session);
+	    const { internetAccounts } = require$$1$3.getRoot(session);
 	    const apolloInternetAccount = internetAccounts.find((ia) => ia.type === 'ApolloInternetAccount');
 	    if (!apolloInternetAccount) {
 	        throw new Error('No Apollo internet account found');
@@ -38564,7 +38845,7 @@
 	}
 
 	function ViewCheckResults({ handleClose, session, }) {
-	    const { internetAccounts } = require$$1$4.getRoot(session);
+	    const { internetAccounts } = require$$1$3.getRoot(session);
 	    const { collaborationServerDriver } = session.apolloDataStore;
 	    const apolloInternetAccount = internetAccounts.find((ia) => ia.type === 'ApolloInternetAccount');
 	    if (!apolloInternetAccount) {
@@ -38815,7 +39096,7 @@
 	            setLoginTypes(data);
 	        }
 	        getAuthTypes().catch((error) => {
-	            require$$1$3.isAbortException(error) ? '' : setErrorMessage(String(error));
+	            require$$1$2.isAbortException(error) ? '' : setErrorMessage(String(error));
 	        });
 	        return () => {
 	            controller.abort();
@@ -38861,7 +39142,7 @@
 	const stateModelFactory$2 = (configSchema) => {
 	    return pluggableElementTypes.InternetAccount.named('ApolloInternetAccount')
 	        .props({
-	        type: require$$1$4.types.literal('ApolloInternetAccount'),
+	        type: require$$1$3.types.literal('ApolloInternetAccount'),
 	        configuration: configuration.ConfigurationReference(configSchema),
 	    })
 	        .views((self) => ({
@@ -38892,7 +39173,7 @@
 	                const dec = dist$2.getDecodedToken(token);
 	                const { role } = dec;
 	                if (!role && !roleNotificationSent) {
-	                    const { session } = require$$1$4.getRoot(self);
+	                    const { session } = require$$1$3.getRoot(self);
 	                    session.notify('You have registered as a user but have not been given access. Ask your administrator to enable access for your account.', 'warning');
 	                    // notify
 	                    roleNotificationSent = true;
@@ -38936,7 +39217,7 @@
 	                resolve(token);
 	            },
 	            async openAuthWindow(type, resolve, reject) {
-	                const redirectUri = require$$1$3.isElectron
+	                const redirectUri = require$$1$2.isElectron
 	                    ? 'http://localhost/auth'
 	                    : window.location.origin + window.location.pathname;
 	                const url = new URL('auth/login', self.baseURL);
@@ -38946,7 +39227,7 @@
 	                });
 	                url.search = params.toString();
 	                const eventName = `JBrowseAuthWindow-${self.internetAccountId}`;
-	                if (require$$1$3.isElectron) {
+	                if (require$$1$2.isElectron) {
 	                    const { ipcRenderer } = window.require('electron');
 	                    const redirectUriFromElectron = await ipcRenderer.invoke('openAuthWindow', {
 	                        internetAccountId: self.internetAccountId,
@@ -38969,7 +39250,7 @@
 	        async getTokenFromUser(resolve, reject) {
 	            const { baseURL } = self;
 	            const authType = await new Promise((resolve, reject) => {
-	                const { session } = require$$1$4.getRoot(self);
+	                const { session } = require$$1$3.getRoot(self);
 	                const { baseURL, name } = self;
 	                session.queueDialog((doneCallback) => [
 	                    AuthTypeSelector,
@@ -39019,7 +39300,7 @@
 	        },
 	    }))
 	        .actions((self) => ({
-	        updateLastChangeSequenceNumber: require$$1$4.flow(function* updateLastChangeSequenceNumber() {
+	        updateLastChangeSequenceNumber: require$$1$3.flow(function* updateLastChangeSequenceNumber() {
 	            const { baseURL } = self;
 	            const url = new URL('changes', baseURL);
 	            const searchParams = new URLSearchParams({ limit: '1' });
@@ -39038,8 +39319,8 @@
 	            const sequence = changes.length > 0 ? changes[0].sequence : 0;
 	            self.setLastChangeSequenceNumber(sequence);
 	        }),
-	        getMissingChanges: require$$1$4.flow(function* getMissingChanges() {
-	            const { session } = require$$1$4.getRoot(self);
+	        getMissingChanges: require$$1$3.flow(function* getMissingChanges() {
+	            const { session } = require$$1$3.getRoot(self);
 	            const { changeManager } = session.apolloDataStore;
 	            if (!self.lastChangeSequenceNumber) {
 	                throw new Error('No LastChangeSequence stored in session. Please, refresh you browser to get last updates from server');
@@ -39074,7 +39355,7 @@
 	    })
 	        .actions((self) => ({
 	        addSocketListeners() {
-	            const { session } = require$$1$4.getRoot(self);
+	            const { session } = require$$1$3.getRoot(self);
 	            const { notify } = session;
 	            const token = self.retrieveToken();
 	            if (!token) {
@@ -39168,10 +39449,10 @@
 	        return { postUserLocation: debouncePostUserLocation(postUserLocation) };
 	    })
 	        .actions((self) => ({
-	        initialize: require$$1$4.flow(function* initialize(role) {
+	        initialize: require$$1$3.flow(function* initialize(role) {
 	            if (role === 'admin') {
-	                const rootModel = require$$1$4.getRoot(self);
-	                if (require$$1$3.isAbstractMenuManager(rootModel)) {
+	                const rootModel = require$$1$3.getRoot(self);
+	                if (require$$1$2.isAbstractMenuManager(rootModel)) {
 	                    addMenuItems(rootModel);
 	                }
 	            }
@@ -39197,7 +39478,7 @@
 	                }
 	                // fires when app transitions from prerender, user returns to the app / tab.
 	                if (document.visibilityState === 'visible') {
-	                    const { session } = require$$1$4.getRoot(self);
+	                    const { session } = require$$1$3.getRoot(self);
 	                    session.broadcastLocations();
 	                }
 	            });
@@ -39210,7 +39491,7 @@
 	                if (inWebWorker$1) {
 	                    return;
 	                }
-	                const { session } = require$$1$4.getRoot(self);
+	                const { session } = require$$1$3.getRoot(self);
 	                // This can be undefined if there is no session loaded, e.g. on
 	                // the start screen
 	                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
@@ -39563,11 +39844,11 @@
 	    const featureSnap = [...features.values()].map((a) => 
 	    // eslint-disable-next-line @typescript-eslint/ban-ts-comment
 	    // @ts-expect-error
-	    [...a.values()].map((f) => require$$1$4.getSnapshot(f)));
+	    [...a.values()].map((f) => require$$1$3.getSnapshot(f)));
 	    const apolloInternetAccount = React.useMemo(() => {
-	        const { internetAccounts } = require$$1$4.getRoot(session);
+	        const { internetAccounts } = require$$1$3.getRoot(session);
 	        const { assemblyName } = region;
-	        const { assemblyManager } = require$$1$3.getSession(displayModel);
+	        const { assemblyManager } = require$$1$2.getSession(displayModel);
 	        const assembly = assemblyManager.get(assemblyName);
 	        if (!assembly) {
 	            throw new Error(`No assembly found with name ${assemblyName}`);
@@ -40220,7 +40501,7 @@
 	}
 
 	const ApolloPluginConfigurationSchema = configuration.ConfigurationSchema('ApolloPlugin', {
-	    ontologies: require$$1$4.types.array(OntologyRecordConfiguration),
+	    ontologies: require$$1$3.types.array(OntologyRecordConfiguration),
 	});
 
 	function parseCigar(cigar) {
@@ -40236,12 +40517,12 @@
 	    const newStateModel = stateModel
 	        .views((self) => ({
 	        getFirstRegion() {
-	            const lgv = require$$1$3.getContainingView(self);
+	            const lgv = require$$1$2.getContainingView(self);
 	            return lgv.dynamicBlocks.contentBlocks[0];
 	        },
 	        getAssembly() {
 	            const firstRegion = self.getFirstRegion();
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            const { assemblyManager } = session;
 	            const { assemblyName } = firstRegion;
 	            const assembly = assemblyManager.get(assemblyName);
@@ -40369,7 +40650,7 @@
 	                assembly: assemblyId,
 	                addedFeature: newFeature,
 	            });
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            await session.apolloDataStore.changeManager.submit(change);
 	            session.notify('Annotation added successfully', 'success');
 	        },
@@ -40482,12 +40763,12 @@
 	        if (key.startsWith('gff_')) {
 	            const newKey = key.slice(4);
 	            const capitalizedKey = newKey.charAt(0).toUpperCase() + newKey.slice(1);
-	            return [capitalizedKey, require$$1$4.getSnapshot(value)];
+	            return [capitalizedKey, require$$1$3.getSnapshot(value)];
 	        }
 	        if (key === '_id') {
-	            return ['ID', require$$1$4.getSnapshot(value)];
+	            return ['ID', require$$1$3.getSnapshot(value)];
 	        }
-	        return [key, require$$1$4.getSnapshot(value)];
+	        return [key, require$$1$3.getSnapshot(value)];
 	    }));
 	    const { notify } = session;
 	    const { changeManager } = session.apolloDataStore;
@@ -40830,7 +41111,7 @@
 	const ApolloFeatureDetailsWidget = mobxReact.observer(function ApolloFeatureDetailsWidget(props) {
 	    const { model } = props;
 	    const { assembly, feature, refName } = model;
-	    const session = require$$1$3.getSession(model);
+	    const session = require$$1$2.getSession(model);
 	    const currentAssembly = session.apolloDataStore.assemblies.get(assembly);
 	    const { classes } = useStyles$8();
 	    if (!(feature && currentAssembly)) {
@@ -41371,7 +41652,7 @@
 	  Object.defineProperty(exports, "__esModule", {
 	    value: true
 	  });
-	  var tslib_1 = require$$0;
+	  var tslib_1 = require$$0$1;
 	  tslib_1.__exportStar(AnnotationFeatureModel, exports);
 	  tslib_1.__exportStar(ApolloAssembly, exports);
 	  tslib_1.__exportStar(ApolloRefSeq, exports);
@@ -41379,18 +41660,18 @@
 	})(dist);
 
 	/* eslint-disable @typescript-eslint/no-unsafe-call */
-	const ApolloFeatureDetailsWidgetModel = require$$1$4.types
+	const ApolloFeatureDetailsWidgetModel = require$$1$3.types
 	    .model('ApolloFeatureDetailsWidget', {
 	    id: mst.ElementId,
-	    type: require$$1$4.types.literal('ApolloFeatureDetailsWidget'),
-	    feature: require$$1$4.types.maybe(require$$1$4.types.reference(dist.AnnotationFeatureModel, {
+	    type: require$$1$3.types.literal('ApolloFeatureDetailsWidget'),
+	    feature: require$$1$3.types.maybe(require$$1$3.types.reference(dist.AnnotationFeatureModel, {
 	        onInvalidated(ev) {
 	            ev.parent.setTryReload(ev.invalidId);
 	            ev.removeRef();
 	        },
 	    })),
-	    assembly: require$$1$4.types.string,
-	    refName: require$$1$4.types.string,
+	    assembly: require$$1$3.types.string,
+	    refName: require$$1$3.types.string,
 	})
 	    .volatile(() => ({
 	    tryReload: undefined,
@@ -41406,11 +41687,11 @@
 	}))
 	    .actions((self) => ({
 	    afterAttach() {
-	        require$$1$4.addDisposer(self, mobx.autorun((reaction) => {
+	        require$$1$3.addDisposer(self, mobx.autorun((reaction) => {
 	            if (!self.tryReload) {
 	                return;
 	            }
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            const { apolloDataStore } = session;
 	            if (!apolloDataStore) {
 	                return;
@@ -41424,19 +41705,19 @@
 	        }));
 	    },
 	}));
-	const ApolloTranscriptDetailsModel = require$$1$4.types
+	const ApolloTranscriptDetailsModel = require$$1$3.types
 	    .model('ApolloTranscriptDetails', {
 	    id: mst.ElementId,
-	    type: require$$1$4.types.literal('ApolloTranscriptDetails'),
-	    feature: require$$1$4.types.maybe(require$$1$4.types.reference(dist.AnnotationFeatureModel, {
+	    type: require$$1$3.types.literal('ApolloTranscriptDetails'),
+	    feature: require$$1$3.types.maybe(require$$1$3.types.reference(dist.AnnotationFeatureModel, {
 	        onInvalidated(ev) {
 	            ev.parent.setTryReload(ev.invalidId);
 	            ev.removeRef();
 	        },
 	    })),
-	    assembly: require$$1$4.types.string,
-	    refName: require$$1$4.types.string,
-	    changeManager: require$$1$4.types.frozen(),
+	    assembly: require$$1$3.types.string,
+	    refName: require$$1$3.types.string,
+	    changeManager: require$$1$3.types.frozen(),
 	})
 	    .volatile(() => ({
 	    tryReload: undefined,
@@ -41452,11 +41733,11 @@
 	}))
 	    .actions((self) => ({
 	    afterAttach() {
-	        require$$1$4.addDisposer(self, mobx.autorun((reaction) => {
+	        require$$1$3.addDisposer(self, mobx.autorun((reaction) => {
 	            if (!self.tryReload) {
 	                return;
 	            }
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            const { apolloDataStore } = session;
 	            if (!apolloDataStore) {
 	                return;
@@ -41593,8 +41874,8 @@
 	                let startSeq = refData.getSequence(Number(dataPoint.min) - 2, Number(dataPoint.min));
 	                let endSeq = refData.getSequence(Number(dataPoint.max), Number(dataPoint.max) + 2);
 	                if (featureNew.strand === -1 && startSeq && endSeq) {
-	                    startSeq = require$$1$3.revcom(startSeq);
-	                    endSeq = require$$1$3.revcom(endSeq);
+	                    startSeq = require$$1$2.revcom(startSeq);
+	                    endSeq = require$$1$2.revcom(endSeq);
 	                }
 	                const oneCDS = {
 	                    id: featureNew._id,
@@ -41790,8 +42071,8 @@
 	            let startSeq = refData.getSequence(Number(currentFeature.min) - 2, Number(currentFeature.min));
 	            let endSeq = refData.getSequence(Number(currentFeature.max), Number(currentFeature.max) + 2);
 	            if (currentFeature.strand === -1 && startSeq && endSeq) {
-	                startSeq = require$$1$3.revcom(startSeq);
-	                endSeq = require$$1$3.revcom(endSeq);
+	                startSeq = require$$1$2.revcom(startSeq);
+	                endSeq = require$$1$2.revcom(endSeq);
 	            }
 	            const oneCDS = {
 	                id: currentFeature._id,
@@ -41889,7 +42170,7 @@
 	                for (const item of transcriptItems) {
 	                    if (item.type === 'CDS') {
 	                        const refSeq = refData.getSequence(Number(item.min + 1), Number(item.max));
-	                        seqData += item.strand === -1 && refSeq ? require$$1$3.revcom(refSeq) : refSeq;
+	                        seqData += item.strand === -1 && refSeq ? require$$1$2.revcom(refSeq) : refSeq;
 	                        textSegments.push({ text: seqData, color: cdsColor });
 	                    }
 	                }
@@ -41902,7 +42183,7 @@
 	                        item.type === 'three_prime_UTR' ||
 	                        item.type === 'five_prime_UTR') {
 	                        const refSeq = refData.getSequence(Number(item.min + 1), Number(item.max));
-	                        seqData += item.strand === -1 && refSeq ? require$$1$3.revcom(refSeq) : refSeq;
+	                        seqData += item.strand === -1 && refSeq ? require$$1$2.revcom(refSeq) : refSeq;
 	                        if (item.type === 'CDS') {
 	                            textSegments.push({ text: seqData, color: cdsColor });
 	                        }
@@ -41927,14 +42208,14 @@
 	                        count != transcriptItems.length) {
 	                        // Intron etc. between CDS/UTRs. No need to check this on very last item
 	                        const refSeq = refData.getSequence(lastEnd + 1, Number(item.min) - 1);
-	                        seqData += item.strand === -1 && refSeq ? require$$1$3.revcom(refSeq) : refSeq;
+	                        seqData += item.strand === -1 && refSeq ? require$$1$2.revcom(refSeq) : refSeq;
 	                        textSegments.push({ text: seqData, color: 'black' });
 	                    }
 	                    if (item.type === 'CDS' ||
 	                        item.type === 'three_prime_UTR' ||
 	                        item.type === 'five_prime_UTR') {
 	                        const refSeq = refData.getSequence(Number(item.min + 1), Number(item.max));
-	                        seqData += item.strand === -1 && refSeq ? require$$1$3.revcom(refSeq) : refSeq;
+	                        seqData += item.strand === -1 && refSeq ? require$$1$2.revcom(refSeq) : refSeq;
 	                        switch (item.type) {
 	                            case 'CDS': {
 	                                textSegments.push({ text: seqData, color: cdsColor });
@@ -42010,10 +42291,10 @@
 	    const { classes } = useStyles$7();
 	    const { model } = props;
 	    const { assembly, feature, refName } = model;
-	    const session = require$$1$3.getSession(model);
-	    const apolloSession = require$$1$3.getSession(model);
+	    const session = require$$1$2.getSession(model);
+	    const apolloSession = require$$1$2.getSession(model);
 	    const currentAssembly = apolloSession.apolloDataStore.assemblies.get(assembly);
-	    const { internetAccounts } = require$$1$4.getRoot(session);
+	    const { internetAccounts } = require$$1$3.getRoot(session);
 	    const apolloInternetAccount = internetAccounts.find((ia) => ia.type === 'ApolloInternetAccount');
 	    const role = apolloInternetAccount ? apolloInternetAccount.role : 'admin';
 	    const editable = ['admin', 'user'].includes(role ?? '');
@@ -42111,12 +42392,12 @@
 	        if (key.startsWith('gff_')) {
 	            const newKey = key.slice(4);
 	            const capitalizedKey = newKey.charAt(0).toUpperCase() + newKey.slice(1);
-	            return [capitalizedKey, require$$1$4.getSnapshot(value)];
+	            return [capitalizedKey, require$$1$3.getSnapshot(value)];
 	        }
 	        if (key === '_id') {
-	            return ['ID', require$$1$4.getSnapshot(value)];
+	            return ['ID', require$$1$3.getSnapshot(value)];
 	        }
-	        return [key, require$$1$4.getSnapshot(value)];
+	        return [key, require$$1$3.getSnapshot(value)];
 	    })
 	        .filter(([key]) => key) // Leave empty keys off
 	        .map(([key, values]) => `${key}=${Array.isArray(values) ? values.join(', ') : values}`)
@@ -42215,7 +42496,7 @@
 	                ]);
 	            },
 	        });
-	        if (feature.type === 'mRNA' && require$$1$3.isSessionModelWithWidgets(session)) {
+	        if (feature.type === 'mRNA' && require$$1$2.isSessionModelWithWidgets(session)) {
 	            menuItems.push({
 	                label: 'Edit transcript details',
 	                onClick: () => {
@@ -42293,9 +42574,9 @@
 	 * #stateModel TrackHeightMixin
 	 * #category display
 	 */
-	const TrackHeightMixin = require$$1$4.types
+	const TrackHeightMixin = require$$1$3.types
 	    .model({
-	    heightPreConfig: require$$1$4.types.maybe(require$$1$4.types.refinement('displayHeight', require$$1$4.types.number, (n) => n >= minDisplayHeight)),
+	    heightPreConfig: require$$1$3.types.maybe(require$$1$3.types.refinement('displayHeight', require$$1$3.types.number, (n) => n >= minDisplayHeight)),
 	})
 	    .volatile(() => ({
 	    scrollTop: 0,
@@ -42327,15 +42608,15 @@
 	    //   'LinearGenomeViewPlugin',
 	    // ) as LinearGenomeViewPlugin
 	    // const { TrackHeightMixin } = LGVPlugin.exports
-	    return require$$1$4.types
+	    return require$$1$3.types
 	        .compose(pluggableElementTypes.BaseDisplay, TrackHeightMixin)
 	        .named('BaseLinearApolloDisplay')
 	        .props({
-	        type: require$$1$4.types.literal('LinearApolloDisplay'),
+	        type: require$$1$3.types.literal('LinearApolloDisplay'),
 	        configuration: configuration.ConfigurationReference(configSchema),
 	    })
 	        .volatile((self) => ({
-	        lgv: require$$1$3.getContainingView(self),
+	        lgv: require$$1$2.getContainingView(self),
 	    }))
 	        .views((self) => {
 	        const { configuration, renderProps: superRenderProps } = self;
@@ -42354,7 +42635,7 @@
 	            return self.configuration.renderer.type;
 	        },
 	        get session() {
-	            return require$$1$3.getSession(self);
+	            return require$$1$2.getSession(self);
 	        },
 	        get regions() {
 	            const regions = self.lgv.dynamicBlocks.contentBlocks.map(({ assemblyName, end, refName, start }) => ({
@@ -42375,7 +42656,7 @@
 	        .views((self) => ({
 	        get apolloInternetAccount() {
 	            const [region] = self.regions;
-	            const { internetAccounts } = require$$1$4.getRoot(self);
+	            const { internetAccounts } = require$$1$3.getRoot(self);
 	            const { assemblyName } = region;
 	            const { assemblyManager } = self.session;
 	            const assembly = assemblyManager.get(assemblyName);
@@ -42410,7 +42691,7 @@
 	            self.session.apolloSetSelectedFeature(feature);
 	        },
 	        afterAttach() {
-	            require$$1$4.addDisposer(self, mobx.autorun(() => {
+	            require$$1$3.addDisposer(self, mobx.autorun(() => {
 	                if (!self.lgv.initialized || self.regionCannotBeRendered()) {
 	                    return;
 	                }
@@ -42441,7 +42722,7 @@
 	                const { end, refName, start } = region;
 	                for (const [, feature] of self.seenFeatures) {
 	                    if (refName !== assembly?.getCanonicalRefName(feature.refSeq) ||
-	                        !require$$1$3.doesIntersect2(start, end, feature.min, feature.max) ||
+	                        !require$$1$2.doesIntersect2(start, end, feature.min, feature.max) ||
 	                        feature.length > self.featuresMinMaxLimit) {
 	                        continue;
 	                    }
@@ -42487,12 +42768,12 @@
 	                const rows = [];
 	                const { end, refName, start } = region;
 	                for (const [id, feature] of self.seenFeatures.entries()) {
-	                    if (!require$$1$4.isAlive(feature)) {
+	                    if (!require$$1$3.isAlive(feature)) {
 	                        self.deleteSeenFeature(id);
 	                        continue;
 	                    }
 	                    if (refName !== assembly?.getCanonicalRefName(feature.refSeq) ||
-	                        !require$$1$3.doesIntersect2(start, end, feature.min, feature.max)) {
+	                        !require$$1$2.doesIntersect2(start, end, feature.min, feature.max)) {
 	                        continue;
 	                    }
 	                    const rowCount = getGlyph(feature).getRowCount(feature, self.lgv.bpPerPx);
@@ -42582,7 +42863,7 @@
 	    }))
 	        .actions((self) => ({
 	        afterAttach() {
-	            require$$1$4.addDisposer(self, mobx.autorun(() => {
+	            require$$1$3.addDisposer(self, mobx.autorun(() => {
 	                if (!self.lgv.initialized || self.regionCannotBeRendered()) {
 	                    return;
 	                }
@@ -42594,7 +42875,7 @@
 	                        continue;
 	                    }
 	                    for (const [, feature] of features) {
-	                        if (require$$1$3.doesIntersect2(region.start, region.end, feature.min, feature.max) &&
+	                        if (require$$1$2.doesIntersect2(region.start, region.end, feature.min, feature.max) &&
 	                            !self.seenFeatures.has(feature._id)) {
 	                            self.addSeenFeature(feature);
 	                        }
@@ -42658,7 +42939,7 @@
 	            self.theme = theme;
 	        },
 	        afterAttach() {
-	            require$$1$4.addDisposer(self, mobx.autorun(() => {
+	            require$$1$3.addDisposer(self, mobx.autorun(() => {
 	                if (!self.lgv.initialized || self.regionCannotBeRendered()) {
 	                    return;
 	                }
@@ -42713,7 +42994,7 @@
 	}
 	function reverseCodonSeq(seq) {
 	    return [...seq]
-	        .map((c) => require$$1$3.revcom(c))
+	        .map((c) => require$$1$2.revcom(c))
 	        .reverse()
 	        .join('');
 	}
@@ -42730,7 +43011,7 @@
 	    if (reverse) {
 	        codonSeq = reverseCodonSeq(codonSeq);
 	    }
-	    const codonLetter = require$$1$3.defaultCodonTable[codonSeq];
+	    const codonLetter = require$$1$2.defaultCodonTable[codonSeq];
 	    if (!codonLetter) {
 	        return;
 	    }
@@ -42749,7 +43030,7 @@
 	    const LinearApolloDisplayRendering = renderingModelIntermediateFactory(pluginManager, configSchema);
 	    return LinearApolloDisplayRendering.actions((self) => ({
 	        afterAttach() {
-	            require$$1$4.addDisposer(self, mobx.autorun(async () => {
+	            require$$1$3.addDisposer(self, mobx.autorun(async () => {
 	                if (!self.lgv.initialized || self.regionCannotBeRendered()) {
 	                    return;
 	                }
@@ -42818,7 +43099,7 @@
 	                                drawLetter(seqTrackctx, startPx, widthPx, letter, self.sequenceRowHeight * 3);
 	                            }
 	                            // Draw reverse
-	                            const revLetter = require$$1$3.revcom(letter);
+	                            const revLetter = require$$1$2.revcom(letter);
 	                            seqTrackctx.beginPath();
 	                            seqTrackctx.fillStyle = colorCode(revLetter, self.theme);
 	                            seqTrackctx.rect(startPx, self.sequenceRowHeight * 4, widthPx, self.sequenceRowHeight);
@@ -42845,7 +43126,7 @@
 	    const LinearApolloDisplayRendering = sequenceRenderingModelFactory(pluginManager, configSchema);
 	    return LinearApolloDisplayRendering.actions((self) => ({
 	        afterAttach() {
-	            require$$1$4.addDisposer(self, mobx.autorun(() => {
+	            require$$1$3.addDisposer(self, mobx.autorun(() => {
 	                const { canvas, featureLayouts, featuresHeight, lgv } = self;
 	                if (!lgv.initialized || self.regionCannotBeRendered()) {
 	                    return;
@@ -42863,7 +43144,7 @@
 	                            if (featureRow > 0) {
 	                                continue;
 	                            }
-	                            if (!require$$1$3.doesIntersect2(displayedRegion.start, displayedRegion.end, feature.min, feature.max)) {
+	                            if (!require$$1$2.doesIntersect2(displayedRegion.start, displayedRegion.end, feature.min, feature.max)) {
 	                                continue;
 	                            }
 	                            getGlyph(feature).draw(ctx, feature, row, self, idx);
@@ -42990,7 +43271,7 @@
 	    const LinearApolloDisplayRendering = mouseEventsModelIntermediateFactory(pluginManager, configSchema);
 	    return LinearApolloDisplayRendering.actions((self) => ({
 	        afterAttach() {
-	            require$$1$4.addDisposer(self, mobx.autorun(() => {
+	            require$$1$3.addDisposer(self, mobx.autorun(() => {
 	                // This type is wrong in @jbrowse/core
 	                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
 	                if (!self.lgv.initialized || self.regionCannotBeRendered()) {
@@ -43018,7 +43299,7 @@
 	                            continue;
 	                        }
 	                        for (const dl of cdsLocs) {
-	                            const frame = require$$1$3.getFrame(dl.min, dl.max, feature.strand ?? 1, dl.phase);
+	                            const frame = require$$1$2.getFrame(dl.min, dl.max, feature.strand ?? 1, dl.phase);
 	                            const row = getTranslationRow(frame, lgv.bpPerPx);
 	                            const offset = (lgv.bpToPx({
 	                                refName: region.refName,
@@ -43162,7 +43443,7 @@
 	    }))
 	        .actions((self) => ({
 	        afterAttach() {
-	            require$$1$4.addDisposer(self, mobx.autorun(() => {
+	            require$$1$3.addDisposer(self, mobx.autorun(() => {
 	                // This type is wrong in @jbrowse/core
 	                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
 	                if (!self.lgv.initialized || self.regionCannotBeRendered()) {
@@ -43680,7 +43961,7 @@
 	                ctx.fillRect(cdsStartPx, cdsTop, cdsWidthPx, cdsHeight);
 	                if (cdsWidthPx > 2) {
 	                    ctx.clearRect(cdsStartPx + 1, cdsTop + 1, cdsWidthPx - 2, cdsHeight - 2);
-	                    const frame = require$$1$3.getFrame(cds.min, cds.max, child.strand ?? 1, cds.phase);
+	                    const frame = require$$1$2.getFrame(cds.min, cds.max, child.strand ?? 1, cds.phase);
 	                    const frameColor = theme?.palette.framesCDS.at(frame)?.main;
 	                    const cdsColorCode = frameColor ?? 'rgb(171,71,188)';
 	                    ctx.fillStyle =
@@ -43894,7 +44175,7 @@
 	        }
 	        const exonChildren = [...mRNA.children.values()].filter((child) => child.type === 'exon');
 	        const overlappingExon = exonChildren.find((child) => {
-	            const [start, end] = require$$1$3.intersection2(bp, bp + 1, child.min, child.max);
+	            const [start, end] = require$$1$2.intersection2(bp, bp + 1, child.min, child.max);
 	            return start !== undefined && end !== undefined;
 	        });
 	        if (!overlappingExon) {
@@ -44378,10 +44659,10 @@
 	        React__default["default"].createElement(HybridGrid, { model: displayState })));
 	});
 
-	const TabularEditorStateModelType = require$$1$4.types
+	const TabularEditorStateModelType = require$$1$3.types
 	    .model('TabularEditor', {
 	    isShown: true,
-	    featureCollapsed: require$$1$4.types.map(require$$1$4.types.boolean),
+	    featureCollapsed: require$$1$3.types.map(require$$1$3.types.boolean),
 	    filterText: '',
 	})
 	    .actions((self) => ({
@@ -44396,7 +44677,7 @@
 	    },
 	    collapseAllFeatures() {
 	        // iterate over all seen features and set them to collapsed
-	        const display = require$$1$4.getParent(self);
+	        const display = require$$1$3.getParent(self);
 	        for (const [featureId] of display.seenFeatures.entries()) {
 	            self.featureCollapsed.set(featureId, true);
 	        }
@@ -44419,7 +44700,7 @@
 	    // TODO: this needs to be refactored so that the final composition of the
 	    // state model mixins happens here in one central place
 	    return mouseEventsModelFactory(pluginManager, configSchema)
-	        .props({ tabularEditor: require$$1$4.types.optional(TabularEditorStateModelType, {}) })
+	        .props({ tabularEditor: require$$1$3.types.optional(TabularEditorStateModelType, {}) })
 	        .named('LinearApolloDisplay');
 	}
 
@@ -44490,7 +44771,7 @@
 	    const { model } = props;
 	    const { apolloRowHeight, contextMenuItems: getContextMenuItems, cursor, featuresHeight, isShown, onMouseDown, onMouseLeave, onMouseMove, onMouseUp, regionCannotBeRendered, session, setCanvas, setCollaboratorCanvas, setOverlayCanvas, setSeqTrackCanvas, setSeqTrackOverlayCanvas, setTheme, tabularEditor, } = model;
 	    const { classes } = useStyles$1();
-	    const lgv = require$$1$3.getContainingView(model);
+	    const lgv = require$$1$2.getContainingView(model);
 	    React.useEffect(() => {
 	        setTheme(theme);
 	    }, [theme, setTheme]);
@@ -44554,7 +44835,7 @@
 	                    .filter((checkResult) => assembly?.isValidRefName(checkResult.refSeq) &&
 	                    assembly.getCanonicalRefName(checkResult.refSeq) ===
 	                        region.refName &&
-	                    require$$1$3.doesIntersect2(region.start, region.end, checkResult.start, checkResult.end))
+	                    require$$1$2.doesIntersect2(region.start, region.end, checkResult.start, checkResult.end))
 	                    .map((checkResult) => {
 	                    const left = (lgv.bpToPx({
 	                        refName: region.refName,
@@ -44741,15 +45022,15 @@
 	default_1 = Save["default"] = _default;
 
 	/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-	const ApolloJobModel = require$$1$4.types
+	const ApolloJobModel = require$$1$3.types
 	    .model('JobsManager', {})
 	    .views((self) => ({
 	    get jobStatusWidget() {
-	        const { widgets } = require$$1$3.getSession(self);
+	        const { widgets } = require$$1$2.getSession(self);
 	        let jobStatusWidget = widgets.get('JobsList');
 	        if (!jobStatusWidget) {
 	            // @ts-expect-error: addWidget function not detected on the session
-	            jobStatusWidget = require$$1$3.getSession(self).addWidget('JobsListWidget', 'JobsList');
+	            jobStatusWidget = require$$1$2.getSession(self).addWidget('JobsListWidget', 'JobsList');
 	        }
 	        return jobStatusWidget;
 	    },
@@ -44773,8 +45054,8 @@
 	     * @param msg - a message to communicate to the user about the abort operation
 	     */
 	    abortJob(jobName, msg) {
-	        const session = require$$1$3.getSession(self);
-	        if (require$$1$3.isSessionModelWithWidgets(session)) {
+	        const session = require$$1$2.getSession(self);
+	        if (require$$1$2.isSessionModelWithWidgets(session)) {
 	            session.showWidget(self.jobStatusWidget);
 	            self.jobStatusWidget.updateJobStatusMessage(jobName, msg ?? 'Aborted unexpectedly');
 	            // this is done to avoid issues with reusing nodes from other state trees
@@ -44792,8 +45073,8 @@
 	     * @param job - the job to be run within the JobsManager
 	     */
 	    runJob(job) {
-	        const session = require$$1$3.getSession(self);
-	        if (require$$1$3.isSessionModelWithWidgets(session)) {
+	        const session = require$$1$2.getSession(self);
+	        if (require$$1$2.isSessionModelWithWidgets(session)) {
 	            session.showWidget(self.jobStatusWidget);
 	            self.jobStatusWidget.addJob(job);
 	        }
@@ -44806,8 +45087,8 @@
 	     * @param job - the job to be completed
 	     */
 	    done(job) {
-	        const session = require$$1$3.getSession(self);
-	        if (require$$1$3.isSessionModelWithWidgets(session)) {
+	        const session = require$$1$2.getSession(self);
+	        if (require$$1$2.isSessionModelWithWidgets(session)) {
 	            session.showWidget(self.jobStatusWidget);
 	            // this.setProgressPct(100)
 	            self.jobStatusWidget.removeJob(job.name);
@@ -44838,9 +45119,9 @@
 	    async submit(change, opts = {}) {
 	        const { addToRecents = true, submitToBackend = true, updateJobsManager = false, } = opts;
 	        // pre-validate
-	        const session = require$$1$3.getSession(this.dataStore);
+	        const session = require$$1$2.getSession(this.dataStore);
 	        const controller = new AbortController();
-	        const { jobsManager } = require$$1$3.getSession(this.dataStore);
+	        const { jobsManager } = require$$1$2.getSession(this.dataStore);
 	        const job = {
 	            name: change.typeName,
 	            statusMessage: 'Pre-validating',
@@ -44932,7 +45213,7 @@
 	    async revertLastChange() {
 	        const lastChange = this.recentChanges.pop();
 	        if (!lastChange) {
-	            const session = require$$1$3.getSession(this.dataStore);
+	            const session = require$$1$2.getSession(this.dataStore);
 	            session.notify('No changes to undo!', 'warning');
 	            return;
 	        }
@@ -44974,7 +45255,7 @@
 	     */
 	    async getFeatures(region) {
 	        const { assemblyName, end, refName, start } = region;
-	        const { assemblyManager } = require$$1$3.getSession(this.clientStore);
+	        const { assemblyManager } = require$$1$2.getSession(this.clientStore);
 	        const assembly = assemblyManager.get(assemblyName);
 	        if (!assembly) {
 	            throw new Error(`Could not find assembly with name "${assemblyName}"`);
@@ -45033,7 +45314,7 @@
 	        const inFlightKey = `${region.refName}:${region.start}-${region.end}`;
 	        const inFlightPromise = this.inFlight.get(inFlightKey);
 	        const { assemblyName, end, refName, start } = region;
-	        const { assemblyManager } = require$$1$3.getSession(this.clientStore);
+	        const { assemblyManager } = require$$1$2.getSession(this.clientStore);
 	        const assembly = assemblyManager.get(assemblyName);
 	        if (!assembly) {
 	            throw new Error(`Could not find assembly with name "${assemblyName}"`);
@@ -45093,7 +45374,7 @@
 	        return seq;
 	    }
 	    async getRefNameAliases(assemblyName) {
-	        const { assemblyManager } = require$$1$3.getSession(this.clientStore);
+	        const { assemblyManager } = require$$1$2.getSession(this.clientStore);
 	        const assembly = assemblyManager.get(assemblyName);
 	        if (!assembly) {
 	            throw new Error(`Could not find assembly with name "${assemblyName}"`);
@@ -45125,7 +45406,7 @@
 	        });
 	    }
 	    async getRegions(assemblyName) {
-	        const { assemblyManager } = require$$1$3.getSession(this.clientStore);
+	        const { assemblyManager } = require$$1$2.getSession(this.clientStore);
 	        const assembly = assemblyManager.get(assemblyName);
 	        if (!assembly) {
 	            throw new Error(`Could not find assembly with name "${assemblyName}"`);
@@ -45155,7 +45436,7 @@
 	        }));
 	    }
 	    getAssemblies(internetAccountId) {
-	        const { assemblyManager } = require$$1$3.getSession(this.clientStore);
+	        const { assemblyManager } = require$$1$2.getSession(this.clientStore);
 	        return assemblyManager.assemblies.filter((assembly) => {
 	            const sequenceMetadata = configuration.getConf(assembly, ['sequence', 'metadata']);
 	            if (sequenceMetadata &&
@@ -45240,7 +45521,7 @@
 	        return regions;
 	    }
 	    getAssemblies() {
-	        const { assemblyManager } = require$$1$3.getSession(this.clientStore);
+	        const { assemblyManager } = require$$1$2.getSession(this.clientStore);
 	        return assemblyManager.assemblies.filter((assembly) => {
 	            const sequenceMetadata = configuration.getConf(assembly, ['sequence', 'metadata']);
 	            return Boolean(sequenceMetadata &&
@@ -45260,7 +45541,7 @@
 	/* eslint-disable @typescript-eslint/require-await */
 	class DesktopFileDriver extends BackendDriver {
 	    async loadAssembly(assemblyName) {
-	        const { assemblyManager } = require$$1$3.getSession(this.clientStore);
+	        const { assemblyManager } = require$$1$2.getSession(this.clientStore);
 	        const assembly = assemblyManager.get(assemblyName);
 	        if (!assembly) {
 	            throw new Error(`Assembly ${assemblyName} not found`);
@@ -45318,7 +45599,7 @@
 	        return regions;
 	    }
 	    getAssemblies() {
-	        const { assemblyManager } = require$$1$3.getSession(this.clientStore);
+	        const { assemblyManager } = require$$1$2.getSession(this.clientStore);
 	        return assemblyManager.assemblies.filter((assembly) => {
 	            const sequenceMetadata = configuration.getConf(assembly, ['sequence', 'metadata']);
 	            return Boolean(sequenceMetadata &&
@@ -45331,7 +45612,7 @@
 	        if (!dist$3.isAssemblySpecificChange(change)) {
 	            throw new Error(`Cannot use this type of change with local file: "${change.typeName}"`);
 	        }
-	        const { assemblyManager } = require$$1$3.getSession(this.clientStore);
+	        const { assemblyManager } = require$$1$2.getSession(this.clientStore);
 	        const assembly = assemblyManager.get(change.assembly);
 	        if (!assembly) {
 	            throw new Error(`Could not find assembly with name "${change.assembly}"`);
@@ -45363,7 +45644,7 @@
 	        for (const [, refSeq] of clientAssembly.refSeqs) {
 	            const { features } = refSeq;
 	            for (const [, feature] of features) {
-	                gff3Items.push(dist$2.makeGFF3Feature(require$$1$4.getSnapshot(feature)));
+	                gff3Items.push(dist$2.makeGFF3Feature(require$$1$3.getSnapshot(feature)));
 	            }
 	        }
 	        for (const [, refSeq] of clientAssembly.refSeqs) {
@@ -45388,22 +45669,22 @@
 	}
 
 	function clientDataStoreFactory(AnnotationFeatureExtended) {
-	    return require$$1$4.types
+	    return require$$1$3.types
 	        .model('ClientDataStore', {
-	        typeName: require$$1$4.types.optional(require$$1$4.types.literal('Client'), 'Client'),
-	        assemblies: require$$1$4.types.map(dist.ApolloAssembly),
-	        checkResults: require$$1$4.types.map(dist.CheckResult),
+	        typeName: require$$1$3.types.optional(require$$1$3.types.literal('Client'), 'Client'),
+	        assemblies: require$$1$3.types.map(dist.ApolloAssembly),
+	        checkResults: require$$1$3.types.map(dist.CheckResult),
 	    })
 	        .views((self) => ({
 	        get internetAccounts() {
-	            return require$$1$4.getRoot(self).internetAccounts;
+	            return require$$1$3.getRoot(self).internetAccounts;
 	        },
 	        get pluginConfiguration() {
-	            return require$$1$4.getRoot(self).jbrowse.configuration
+	            return require$$1$3.getRoot(self).jbrowse.configuration
 	                .ApolloPlugin;
 	        },
 	        getFeature(featureId) {
-	            return require$$1$4.resolveIdentifier(AnnotationFeatureExtended, self.assemblies, featureId);
+	            return require$$1$3.resolveIdentifier(AnnotationFeatureExtended, self.assemblies, featureId);
 	        },
 	    }))
 	        .actions((self) => ({
@@ -45438,7 +45719,7 @@
 	                parent.deleteChild(featureId);
 	            }
 	            else {
-	                const refSeq = require$$1$4.getParentOfType(feature, dist.ApolloRefSeq);
+	                const refSeq = require$$1$3.getParentOfType(feature, dist.ApolloRefSeq);
 	                refSeq.deleteFeature(_id);
 	            }
 	        },
@@ -45463,14 +45744,14 @@
 	        changeManager: new ChangeManager(self),
 	        collaborationServerDriver: new CollaborationServerDriver(self),
 	        inMemoryFileDriver: new InMemoryFileDriver(self),
-	        desktopFileDriver: require$$1$3.isElectron
+	        desktopFileDriver: require$$1$2.isElectron
 	            ? new DesktopFileDriver(self)
 	            : undefined,
 	        ontologyManager: OntologyManagerType.create(),
 	    }))
 	        .actions((self) => ({
 	        afterCreate() {
-	            require$$1$4.addDisposer(self, mobx.autorun(() => {
+	            require$$1$3.addDisposer(self, mobx.autorun(() => {
 	                // Merge in the ontologies from our plugin configuration.
 	                // Ontologies of a given name that are already in the session
 	                // take precedence over the ontologies in the configuration.
@@ -45499,7 +45780,7 @@
 	            if (!assemblyId) {
 	                return self.collaborationServerDriver;
 	            }
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            const { assemblyManager } = session;
 	            const assembly = assemblyManager.get(assemblyId);
 	            if (!assembly) {
@@ -45509,7 +45790,7 @@
 	                'sequence',
 	                'metadata',
 	            ]);
-	            if (require$$1$3.isElectron && file) {
+	            if (require$$1$2.isElectron && file) {
 	                return self.desktopFileDriver;
 	            }
 	            if (internetAccountConfigId) {
@@ -45523,7 +45804,7 @@
 	            }
 	            let configId = internetAccountId;
 	            if (assemblyName && !configId) {
-	                const { assemblyManager } = require$$1$3.getSession(self);
+	                const { assemblyManager } = require$$1$2.getSession(self);
 	                const assembly = assemblyManager.get(assemblyName);
 	                if (!assembly) {
 	                    throw new Error(`No assembly found with name ${assemblyName}`);
@@ -45542,7 +45823,7 @@
 	        },
 	    }))
 	        .actions((self) => ({
-	        loadFeatures: require$$1$4.flow(function* loadFeatures(regions) {
+	        loadFeatures: require$$1$3.flow(function* loadFeatures(regions) {
 	            for (const region of regions) {
 	                const backendDriver = self.getBackendDriver(region.assemblyName);
 	                if (!backendDriver) {
@@ -45574,7 +45855,7 @@
 	                self.addCheckResults(checkResults);
 	            }
 	        }),
-	        loadRefSeq: require$$1$4.flow(function* loadRefSeq(regions) {
+	        loadRefSeq: require$$1$3.flow(function* loadRefSeq(regions) {
 	            for (const region of regions) {
 	                const backendDriver = self.getBackendDriver(region.assemblyName);
 	                if (!backendDriver) {
@@ -45607,9 +45888,9 @@
 	    const ClientDataStore = clientDataStoreFactory(AnnotationFeatureExtended);
 	    const sm = sessionModel
 	        .props({
-	        apolloDataStore: require$$1$4.types.optional(ClientDataStore, { typeName: 'Client' }),
-	        apolloSelectedFeature: require$$1$4.types.safeReference(AnnotationFeatureExtended),
-	        jobsManager: require$$1$4.types.optional(ApolloJobModel, {}),
+	        apolloDataStore: require$$1$3.types.optional(ClientDataStore, { typeName: 'Client' }),
+	        apolloSelectedFeature: require$$1$3.types.safeReference(AnnotationFeatureExtended),
+	        jobsManager: require$$1$3.types.optional(ApolloJobModel, {}),
 	    })
 	        .extend(() => {
 	        const collabs = mobx.observable.array([]);
@@ -45673,7 +45954,7 @@
 	            }
 	        },
 	        broadcastLocations() {
-	            const { internetAccounts } = require$$1$4.getRoot(self);
+	            const { internetAccounts } = require$$1$3.getRoot(self);
 	            const locations = [];
 	            for (const view of self.views) {
 	                if (view.type !== 'LinearGenomeView') {
@@ -45717,16 +45998,16 @@
 	        },
 	    }))
 	        .actions((self) => ({
-	        afterCreate: require$$1$4.flow(function* afterCreate() {
+	        afterCreate: require$$1$3.flow(function* afterCreate() {
 	            // When the initial config.json loads, it doesn't include the Apollo
 	            // tracks, which would result in a potentially invalid session snapshot
 	            // if any tracks are open. Here we copy the session snapshot, apply an
 	            // empty session snapshot, and then restore the original session
 	            // snapshot after the updated config.json loads.
-	            const sessionSnapshot = require$$1$4.getSnapshot(self);
+	            const sessionSnapshot = require$$1$3.getSnapshot(self);
 	            const { id, name } = sessionSnapshot;
-	            require$$1$4.applySnapshot(self, { name, id });
-	            const { internetAccounts, jbrowse } = require$$1$4.getRoot(self);
+	            require$$1$3.applySnapshot(self, { name, id });
+	            const { internetAccounts, jbrowse } = require$$1$3.getRoot(self);
 	            mobx.autorun(() => {
 	                // broadcastLocations() // **** This is not working and therefore we need to duplicate broadcastLocations() -method code here because autorun() does not observe changes otherwise
 	                const locations = [];
@@ -45804,8 +46085,8 @@
 	                    console.error(error);
 	                    continue;
 	                }
-	                require$$1$4.applySnapshot(jbrowse, jbrowseConfig);
-	                require$$1$4.applySnapshot(self, sessionSnapshot);
+	                require$$1$3.applySnapshot(jbrowse, jbrowseConfig);
+	                require$$1$3.applySnapshot(self, sessionSnapshot);
 	            }
 	        }),
 	        beforeDestroy() {
@@ -45829,16 +46110,16 @@
 	                        {
 	                            label: 'Save track to Apollo',
 	                            onClick: async () => {
-	                                const { internetAccounts, jbrowse } = require$$1$4.getRoot(self);
-	                                const currentConfig = require$$1$4.getSnapshot(jbrowse);
+	                                const { internetAccounts, jbrowse } = require$$1$3.getRoot(self);
+	                                const currentConfig = require$$1$3.getSnapshot(jbrowse);
 	                                let filteredConfig;
 	                                filteredConfig = dist$2.filterJBrowseConfig(currentConfig);
 	                                if (Object.keys(filteredConfig).length === 0) {
 	                                    filteredConfig = undefined;
 	                                }
-	                                let trackConfigSnapshot = require$$1$4.getSnapshot(conf);
+	                                const trackConfigSnapshot = require$$1$3.getSnapshot(conf);
 	                                const newTrackId = trackId.slice(0, trackId.length - sessionTrackIdentifier.length);
-	                                trackConfigSnapshot = {
+	                                const newTrackConfigSnapshot = {
 	                                    ...trackConfigSnapshot,
 	                                    trackId: newTrackId,
 	                                };
@@ -45853,7 +46134,7 @@
 	                                            ...filteredConfig,
 	                                            tracks: filteredConfig?.tracks && [
 	                                                ...filteredConfig.tracks,
-	                                                trackConfigSnapshot,
+	                                                newTrackConfigSnapshot,
 	                                            ],
 	                                        },
 	                                    });
@@ -45864,6 +46145,10 @@
 	                                    const { notify } = self;
 	                                    notify('Track added', 'success');
 	                                }
+	                                // @ts-expect-error This method is missing in the JB types
+	                                self.deleteTrackConf(conf);
+	                                // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+	                                jbrowse.addTrackConf(newTrackConfigSnapshot);
 	                            },
 	                            icon: default_1,
 	                        },
@@ -45873,8 +46158,8 @@
 	                        {
 	                            label: 'Remove track from Apollo',
 	                            onClick: async () => {
-	                                const { internetAccounts, jbrowse } = require$$1$4.getRoot(self);
-	                                const currentConfig = require$$1$4.getSnapshot(jbrowse);
+	                                const { internetAccounts, jbrowse } = require$$1$3.getRoot(self);
+	                                const currentConfig = require$$1$3.getSnapshot(jbrowse);
 	                                let filteredConfig;
 	                                filteredConfig = dist$2.filterJBrowseConfig(currentConfig);
 	                                if (Object.keys(filteredConfig).length === 0) {
@@ -45900,6 +46185,10 @@
 	                                    const { notify } = self;
 	                                    notify('Track removed', 'success');
 	                                }
+	                                // @ts-expect-error This method is missing in the JB types
+	                                self.deleteTrackConf(conf);
+	                                // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+	                                jbrowse.deleteTrackConf(conf);
 	                            },
 	                            icon: default_1,
 	                        },
@@ -45907,7 +46196,7 @@
 	            },
 	        };
 	    });
-	    return require$$1$4.types.snapshotProcessor(sm, {
+	    return require$$1$3.types.snapshotProcessor(sm, {
 	        postProcessor(snap) {
 	            snap.apolloSelectedFeature = undefined;
 	            const assemblies = Object.fromEntries(Object.entries(snap.apolloDataStore.assemblies).filter(([, assembly]) => assembly.backendDriverType === 'InMemoryFileDriver'));
@@ -45937,7 +46226,7 @@
 	    const { BaseLinearDisplay } = LGVPlugin.exports;
 	    return BaseLinearDisplay.named('SixFrameFeatureDisplay')
 	        .props({
-	        type: require$$1$4.types.literal('SixFrameFeatureDisplay'),
+	        type: require$$1$3.types.literal('SixFrameFeatureDisplay'),
 	        configuration: configuration.ConfigurationReference(configSchema),
 	        apolloRowHeight: 20,
 	        detailsMinHeight: 200,
@@ -45980,23 +46269,23 @@
 	            return regions;
 	        },
 	        regionCannotBeRendered( /* region */) {
-	            const view = require$$1$3.getContainingView(self);
+	            const view = require$$1$2.getContainingView(self);
 	            if (view && view.bpPerPx >= 200) {
 	                return 'Zoom in to see annotations';
 	            }
 	            return;
 	        },
 	        get session() {
-	            return require$$1$3.getSession(self);
+	            return require$$1$2.getSession(self);
 	        },
 	    }))
 	        .actions((self) => {
 	        let previousBlockKeys = [];
 	        return {
 	            afterAttach() {
-	                require$$1$4.addDisposer(self, mobx.autorun(() => {
-	                    const session = require$$1$3.getSession(self);
-	                    const view = require$$1$3.getContainingView(self);
+	                require$$1$3.addDisposer(self, mobx.autorun(() => {
+	                    const session = require$$1$2.getSession(self);
+	                    const view = require$$1$2.getContainingView(self);
 	                    if (view.initialized) {
 	                        if (self.regionCannotBeRendered()) {
 	                            return;
@@ -46032,12 +46321,12 @@
 	            return self.configuration.renderer.type;
 	        },
 	        get changeManager() {
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            return session.apolloDataStore.changeManager;
 	        },
 	        get sequence() {
 	            const { regions } = self;
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            const seq = new Map();
 	            for (const region of regions) {
 	                const assembly = session.apolloDataStore.assemblies.get(region.assemblyName);
@@ -46049,7 +46338,7 @@
 	        },
 	        get features() {
 	            const { regions } = self;
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            const features = new Map();
 	            for (const region of regions) {
 	                const assembly = session.apolloDataStore.assemblies.get(region.assemblyName);
@@ -46122,7 +46411,7 @@
 	                if (reversed) {
 	                    tilt = (fullSeq.length + fullStart) % 3;
 	                    effectiveFrame = (reversePhaseMap[i] + tilt + 3) % 3;
-	                    seqSliced = require$$1$3.reverse(fullSeq).slice(effectiveFrame);
+	                    seqSliced = require$$1$2.reverse(fullSeq).slice(effectiveFrame);
 	                }
 	                else {
 	                    tilt = 3 - (fullStart % 3);
@@ -46131,14 +46420,14 @@
 	                }
 	                for (let j = 0; j < seqSliced.length; j += 3) {
 	                    const codon = seqSliced.slice(j, j + 3);
-	                    const normalizedCodon = reversed ? require$$1$3.reverse(require$$1$3.revcom(codon)) : codon;
+	                    const normalizedCodon = reversed ? require$$1$2.reverse(require$$1$2.revcom(codon)) : codon;
 	                    const start = reversed
 	                        ? fullStart + seqSliced.length - (3 + j)
 	                        : fullStart + j + effectiveFrame;
-	                    if (require$$1$3.defaultStarts.includes(normalizedCodon.toUpperCase())) {
+	                    if (require$$1$2.defaultStarts.includes(normalizedCodon.toUpperCase())) {
 	                        starts.push(start);
 	                    }
-	                    else if (require$$1$3.defaultStops.includes(normalizedCodon.toUpperCase())) {
+	                    else if (require$$1$2.defaultStops.includes(normalizedCodon.toUpperCase())) {
 	                        stops.push(start);
 	                    }
 	                }
@@ -46208,7 +46497,7 @@
 	            return featureLayout;
 	        },
 	        getAssemblyId(assemblyName) {
-	            const { assemblyManager } = require$$1$3.getSession(self);
+	            const { assemblyManager } = require$$1$2.getSession(self);
 	            const assembly = assemblyManager.get(assemblyName);
 	            if (!assembly) {
 	                throw new Error(`Could not find assembly named ${assemblyName}`);
@@ -46216,17 +46505,17 @@
 	            return assembly.name;
 	        },
 	        get selectedFeature() {
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            return session.apolloSelectedFeature;
 	        },
 	        get setSelectedFeature() {
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            return session.apolloSetSelectedFeature;
 	        },
 	    }))
 	        .actions((self) => ({
 	        setSelectedFeature(feature) {
-	            const session = require$$1$3.getSession(self);
+	            const session = require$$1$2.getSession(self);
 	            session.apolloSetSelectedFeature(feature);
 	        },
 	        setApolloFeatureUnderMouse(feature) {
@@ -46472,7 +46761,7 @@
 	                                    label: 'Add new feature',
 	                                    icon: default_1$a,
 	                                    onClick: () => {
-	                                        const session = require$$1$3.getSession(self);
+	                                        const session = require$$1$2.getSession(self);
 	                                        const { leftOffset, rightOffset } = self;
 	                                        const selectedRegions = self.getSelectedRegions(leftOffset, rightOffset);
 	                                        session.queueDialog((doneCallback) => [
@@ -46561,7 +46850,7 @@
 	        }
 	    }
 	    configure(pluginManager) {
-	        if (require$$1$3.isAbstractMenuManager(pluginManager.rootModel)) {
+	        if (require$$1$2.isAbstractMenuManager(pluginManager.rootModel)) {
 	            pluginManager.rootModel.appendToMenu('Apollo', {
 	                label: 'Download GFF3',
 	                onClick: (session) => {