@jbrowse/plugin-alignments 1.7.3 → 1.7.6

package/dist/LinearPileupDisplay/model.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
@@ -55,11 +55,11 @@ var _excluded = ["uniqueId"];
 
 function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
 
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2["default"])(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || (0, _typeof2.default)(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
 var ColorByTagDlg = /*#__PURE__*/(0, _react.lazy)(function () {
   return Promise.resolve().then(function () {
@@ -100,10 +100,10 @@ var stateModelFactory = function stateModelFactory(configSchema) {
     configuration: (0, _configuration.ConfigurationReference)(configSchema),
     showSoftClipping: false,
     featureHeight: _mobxStateTree.types.maybe(_mobxStateTree.types.number),
-    noSpacing: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
-    fadeLikelihood: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
+    noSpacing: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
+    fadeLikelihood: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
     trackMaxHeight: _mobxStateTree.types.maybe(_mobxStateTree.types.number),
-    mismatchAlpha: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
+    mismatchAlpha: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
     sortedBy: _mobxStateTree.types.maybe(_mobxStateTree.types.model({
       type: _mobxStateTree.types.string,
       pos: _mobxStateTree.types.number,
@@ -125,7 +125,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         value: _mobxStateTree.types.string
       }))
     }), {})
-  }))["volatile"](function () {
+  })).volatile(function () {
     return {
       colorTagMap: _mobx.observable.map({}),
       modificationTagMap: _mobx.observable.map({}),
@@ -155,7 +155,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         var colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
         uniqueModifications.forEach(function (value) {
           if (!self.modificationTagMap.has(value)) {
-            var totalKeys = (0, _toConsumableArray2["default"])(self.modificationTagMap.keys()).length;
+            var totalKeys = (0, _toConsumableArray2.default)(self.modificationTagMap.keys()).length;
             var newColor = colorPalette[totalKeys];
             self.modificationTagMap.set(value, newColor);
           }
@@ -166,7 +166,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         var colorPalette = ['#BBCCEE', 'pink', '#CCDDAA', '#EEEEBB', '#FFCCCC', 'lightblue', 'lightgreen', 'tan', '#CCEEFF', 'lightsalmon'];
         uniqueTag.forEach(function (value) {
           if (!self.colorTagMap.has(value)) {
-            var totalKeys = (0, _toConsumableArray2["default"])(self.colorTagMap.keys()).length;
+            var totalKeys = (0, _toConsumableArray2.default)(self.colorTagMap.keys()).length;
             var newColor = colorPalette[totalKeys];
             self.colorTagMap.set(value, newColor);
           }
@@ -176,93 +176,97 @@ var stateModelFactory = function stateModelFactory(configSchema) {
   }).actions(function (self) {
     return {
       afterAttach: function afterAttach() {
-        (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
-          var _getSession, rpcManager, sortedBy, colorBy, view, uniqueTagSet, uniqueModificationsSet, pos, refName, assemblyName, region;
+        (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
+          var _getSession, rpcManager, view, sortedBy, colorBy, parentTrack, adapterConfig, rendererType, staticBlocks, bpPerPx, uniqueTagSet, adapter, pos, refName, assemblyName;
 
-          return _regenerator["default"].wrap(function _callee$(_context) {
+          return _regenerator.default.wrap(function _callee$(_context) {
             while (1) {
               switch (_context.prev = _context.next) {
                 case 0:
                   _context.prev = 0;
                   _getSession = (0, _util.getSession)(self), rpcManager = _getSession.rpcManager;
-                  sortedBy = self.sortedBy, colorBy = self.colorBy;
-                  view = (0, _util.getContainingView)(self); // continually generate the vc pairing, set and rerender if any
+                  view = (0, _util.getContainingView)(self);
+                  sortedBy = self.sortedBy, colorBy = self.colorBy, parentTrack = self.parentTrack, adapterConfig = self.adapterConfig, rendererType = self.rendererType;
+                  staticBlocks = view.staticBlocks, bpPerPx = view.bpPerPx; // continually generate the vc pairing, set and rerender if any
                   // new values seen
 
                   if (!(colorBy !== null && colorBy !== void 0 && colorBy.tag)) {
-                    _context.next = 9;
+                    _context.next = 10;
                     break;
                   }
 
-                  _context.next = 7;
-                  return (0, _shared.getUniqueTagValues)(self, colorBy, view.staticBlocks);
+                  _context.next = 8;
+                  return (0, _shared.getUniqueTagValues)(self, colorBy, staticBlocks);
 
-                case 7:
+                case 8:
                   uniqueTagSet = _context.sent;
                   self.updateColorTagMap(uniqueTagSet);
 
-                case 9:
+                case 10:
                   if (!((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications')) {
-                    _context.next = 14;
+                    _context.next = 17;
                     break;
                   }
 
-                  _context.next = 12;
-                  return (0, _shared.getUniqueModificationValues)(self, (0, _configuration.getConf)(self.parentTrack, ['adapter']), colorBy, view.staticBlocks);
+                  adapter = (0, _configuration.getConf)(parentTrack, ['adapter']);
+                  _context.t0 = self;
+                  _context.next = 15;
+                  return (0, _shared.getUniqueModificationValues)(self, adapter, colorBy, staticBlocks);
 
-                case 12:
-                  uniqueModificationsSet = _context.sent;
-                  self.updateModificationColorMap(uniqueModificationsSet);
+                case 15:
+                  _context.t1 = _context.sent;
 
-                case 14:
+                  _context.t0.updateModificationColorMap.call(_context.t0, _context.t1);
+
+                case 17:
                   if (!sortedBy) {
-                    _context.next = 23;
+                    _context.next = 25;
                     break;
                   }
 
-                  pos = sortedBy.pos, refName = sortedBy.refName, assemblyName = sortedBy.assemblyName;
-                  region = {
-                    start: pos,
-                    end: pos + 1,
-                    refName: refName,
-                    assemblyName: assemblyName
-                  }; // render just the sorted region first
+                  pos = sortedBy.pos, refName = sortedBy.refName, assemblyName = sortedBy.assemblyName; // render just the sorted region first
 
-                  _context.next = 19;
+                  _context.next = 21;
                   return self.rendererType.renderInClient(rpcManager, _objectSpread({
                     assemblyName: assemblyName,
-                    regions: [region],
-                    adapterConfig: self.adapterConfig,
-                    rendererType: self.rendererType.name,
+                    regions: [{
+                      start: pos,
+                      end: pos + 1,
+                      refName: refName,
+                      assemblyName: assemblyName
+                    }],
+                    adapterConfig: adapterConfig,
+                    rendererType: rendererType.name,
                     sessionId: (0, _tracks.getRpcSessionId)(self),
+                    layoutId: view.id,
                     timeout: 1000000
                   }, self.renderProps()));
 
-                case 19:
+                case 21:
                   self.setReady(true);
-                  self.setCurrBpPerPx(view.bpPerPx);
-                  _context.next = 24;
+                  self.setCurrBpPerPx(bpPerPx);
+                  _context.next = 26;
                   break;
 
-                case 23:
+                case 25:
                   self.setReady(true);
 
-                case 24:
-                  _context.next = 30;
+                case 26:
+                  _context.next = 32;
                   break;
 
-                case 26:
-                  _context.prev = 26;
-                  _context.t0 = _context["catch"](0);
-                  console.error(_context.t0);
-                  self.setError(_context.t0);
+                case 28:
+                  _context.prev = 28;
+                  _context.t2 = _context["catch"](0);
+                  console.error(_context.t2);
+                  self.setError(_context.t2);
 
-                case 30:
+                case 32:
                 case "end":
                   return _context.stop();
               }
             }
-          }, _callee, null, [[0, 26]]);
+          }, _callee, null, [[0, 28]]);
         })), {
           delay: 1000
         }));
@@ -287,10 +291,10 @@ var stateModelFactory = function stateModelFactory(configSchema) {
       copyFeatureToClipboard: function copyFeatureToClipboard(feature) {
         var _feature$toJSON = feature.toJSON(),
             uniqueId = _feature$toJSON.uniqueId,
-            rest = (0, _objectWithoutProperties2["default"])(_feature$toJSON, _excluded);
+            rest = (0, _objectWithoutProperties2.default)(_feature$toJSON, _excluded);
 
         var session = (0, _util.getSession)(self);
-        (0, _copyToClipboard["default"])(JSON.stringify(rest, null, 4));
+        (0, _copyToClipboard.default)(JSON.stringify(rest, null, 4));
         session.notify('Copied to clipboard', 'success');
       },
       toggleSoftClipping: function toggleSoftClipping() {
@@ -387,7 +391,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
         var feat = self.contextMenuFeature;
         var contextMenuItems = feat ? [{
           label: 'Open feature details',
-          icon: _MenuOpen["default"],
+          icon: _MenuOpen.default,
           onClick: function onClick() {
             self.clearFeatureSelection();
 
@@ -408,7 +412,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
       },
 
       get DisplayBlurb() {
-        return _LinearPileupDisplayBlurb["default"];
+        return _LinearPileupDisplayBlurb.default;
       },
 
       renderProps: function renderProps() {
@@ -430,13 +434,135 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           colorTagMap: JSON.parse(JSON.stringify(colorTagMap)),
           modificationTagMap: JSON.parse(JSON.stringify(modificationTagMap)),
           showSoftClip: self.showSoftClipping,
-          config: self.rendererConfig
+          config: self.rendererConfig,
+          onFeatureClick: function onFeatureClick(_, featureId) {
+            return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
+              var session, rpcManager, f, sessionId, _ref3, feature;
+
+              return _regenerator.default.wrap(function _callee2$(_context2) {
+                while (1) {
+                  switch (_context2.prev = _context2.next) {
+                    case 0:
+                      session = (0, _util.getSession)(self);
+                      rpcManager = session.rpcManager;
+                      _context2.prev = 2;
+                      f = featureId || self.featureIdUnderMouse;
+
+                      if (f) {
+                        _context2.next = 8;
+                        break;
+                      }
+
+                      self.clearFeatureSelection();
+                      _context2.next = 14;
+                      break;
+
+                    case 8:
+                      sessionId = (0, _tracks.getRpcSessionId)(self);
+                      _context2.next = 11;
+                      return rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                        featureId: f,
+                        sessionId: sessionId,
+                        layoutId: (0, _util.getContainingView)(self).id,
+                        rendererType: 'PileupRenderer'
+                      });
+
+                    case 11:
+                      _ref3 = _context2.sent;
+                      feature = _ref3.feature;
+
+                      if (feature) {
+                        // @ts-ignore
+                        self.selectFeature(new _util.SimpleFeature(feature));
+                      }
+
+                    case 14:
+                      _context2.next = 20;
+                      break;
+
+                    case 16:
+                      _context2.prev = 16;
+                      _context2.t0 = _context2["catch"](2);
+                      console.error(_context2.t0);
+                      session.notify("".concat(_context2.t0));
+
+                    case 20:
+                    case "end":
+                      return _context2.stop();
+                  }
+                }
+              }, _callee2, null, [[2, 16]]);
+            }))();
+          },
+          onClick: function onClick() {
+            self.clearFeatureSelection();
+          },
+          // similar to click but opens a menu with further options
+          onFeatureContextMenu: function onFeatureContextMenu(_, featureId) {
+            return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+              var session, rpcManager, f, sessionId, _ref4, feature;
+
+              return _regenerator.default.wrap(function _callee3$(_context3) {
+                while (1) {
+                  switch (_context3.prev = _context3.next) {
+                    case 0:
+                      session = (0, _util.getSession)(self);
+                      rpcManager = session.rpcManager;
+                      _context3.prev = 2;
+                      f = featureId || self.featureIdUnderMouse;
+
+                      if (f) {
+                        _context3.next = 8;
+                        break;
+                      }
+
+                      self.clearFeatureSelection();
+                      _context3.next = 14;
+                      break;
+
+                    case 8:
+                      sessionId = (0, _tracks.getRpcSessionId)(self);
+                      _context3.next = 11;
+                      return rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
+                        featureId: f,
+                        sessionId: sessionId,
+                        layoutId: (0, _util.getContainingView)(self).id,
+                        rendererType: 'PileupRenderer'
+                      });
+
+                    case 11:
+                      _ref4 = _context3.sent;
+                      feature = _ref4.feature;
+
+                      if (feature) {
+                        // @ts-ignore
+                        self.setContextMenuFeature(new _util.SimpleFeature(feature));
+                      }
+
+                    case 14:
+                      _context3.next = 20;
+                      break;
+
+                    case 16:
+                      _context3.prev = 16;
+                      _context3.t0 = _context3["catch"](2);
+                      console.error(_context3.t0);
+                      session.notify("".concat(_context3.t0));
+
+                    case 20:
+                    case "end":
+                      return _context3.stop();
+                  }
+                }
+              }, _callee3, null, [[2, 16]]);
+            }))();
+          }
         });
       },
       trackMenuItems: function trackMenuItems() {
-        return [].concat((0, _toConsumableArray2["default"])(superTrackMenuItems()), [{
+        return [].concat((0, _toConsumableArray2.default)(superTrackMenuItems()), [{
           label: 'Show soft clipping',
-          icon: _Visibility["default"],
+          icon: _Visibility.default,
           type: 'checkbox',
           checked: self.showSoftClipping,
           onClick: function onClick() {
@@ -449,9 +575,9 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           }
         }, {
           label: 'Sort by',
-          icon: _Sort["default"],
+          icon: _Sort.default,
           disabled: self.showSoftClipping,
-          subMenu: [].concat((0, _toConsumableArray2["default"])(['Start location', 'Read strand', 'Base pair'].map(function (option) {
+          subMenu: [].concat((0, _toConsumableArray2.default)(['Start location', 'Read strand', 'Base pair'].map(function (option) {
             return {
               label: option,
               onClick: function onClick() {
@@ -476,7 +602,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           }])
         }, {
           label: 'Color scheme',
-          icon: _Palette["default"],
+          icon: _Palette.default,
           subMenu: [{
             label: 'Normal',
             onClick: function onClick() {
@@ -556,7 +682,7 @@ var stateModelFactory = function stateModelFactory(configSchema) {
           }]
         }, {
           label: 'Filter by',
-          icon: _ClearAll["default"],
+          icon: _ClearAll.default,
           onClick: function onClick() {
             (0, _util.getSession)(self).queueDialog(function (doneCallback) {
               return [FilterByTagDlg, {
@@ -599,4 +725,4 @@ var stateModelFactory = function stateModelFactory(configSchema) {
 };
 
 var _default = stateModelFactory;
-exports["default"] = _default;
+exports.default = _default;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _extends2 = _interopRequireDefault(require("@babel/runtime/helpers/extends"));
 
@@ -22,7 +22,7 @@ var en = function en(n) {
   return n.toLocaleString('en-US');
 };
 
-var TooltipContents = /*#__PURE__*/_react["default"].forwardRef(function (_ref, ref) {
+var TooltipContents = /*#__PURE__*/_react.default.forwardRef(function (_ref, ref) {
   var feature = _ref.feature;
   var start = feature.get('start');
   var end = feature.get('end');
@@ -32,22 +32,22 @@ var TooltipContents = /*#__PURE__*/_react["default"].forwardRef(function (_ref,
     return !!f;
   }).join(':');
   var total = info === null || info === void 0 ? void 0 : info.total;
-  return /*#__PURE__*/_react["default"].createElement("div", {
+  return /*#__PURE__*/_react.default.createElement("div", {
     ref: ref
-  }, /*#__PURE__*/_react["default"].createElement("table", null, /*#__PURE__*/_react["default"].createElement("caption", null, loc), /*#__PURE__*/_react["default"].createElement("thead", null, /*#__PURE__*/_react["default"].createElement("tr", null, /*#__PURE__*/_react["default"].createElement("th", null, "Base"), /*#__PURE__*/_react["default"].createElement("th", null, "Count"), /*#__PURE__*/_react["default"].createElement("th", null, "% of Total"), /*#__PURE__*/_react["default"].createElement("th", null, "Strands"), /*#__PURE__*/_react["default"].createElement("th", null, "Source"))), /*#__PURE__*/_react["default"].createElement("tbody", null, /*#__PURE__*/_react["default"].createElement("tr", null, /*#__PURE__*/_react["default"].createElement("td", null, "Total"), /*#__PURE__*/_react["default"].createElement("td", null, total), /*#__PURE__*/_react["default"].createElement("td", null)), Object.entries(info).map(function (_ref2) {
-    var _ref3 = (0, _slicedToArray2["default"])(_ref2, 2),
+  }, /*#__PURE__*/_react.default.createElement("table", null, /*#__PURE__*/_react.default.createElement("caption", null, loc), /*#__PURE__*/_react.default.createElement("thead", null, /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("th", null, "Base"), /*#__PURE__*/_react.default.createElement("th", null, "Count"), /*#__PURE__*/_react.default.createElement("th", null, "% of Total"), /*#__PURE__*/_react.default.createElement("th", null, "Strands"), /*#__PURE__*/_react.default.createElement("th", null, "Source"))), /*#__PURE__*/_react.default.createElement("tbody", null, /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("td", null, "Total"), /*#__PURE__*/_react.default.createElement("td", null, total), /*#__PURE__*/_react.default.createElement("td", null)), Object.entries(info).map(function (_ref2) {
+    var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
         key = _ref3[0],
         entry = _ref3[1];
 
     return Object.entries(entry).map(function (_ref4) {
-      var _ref5 = (0, _slicedToArray2["default"])(_ref4, 2),
+      var _ref5 = (0, _slicedToArray2.default)(_ref4, 2),
           base = _ref5[0],
           score = _ref5[1];
 
       var strands = score.strands;
-      return /*#__PURE__*/_react["default"].createElement("tr", {
+      return /*#__PURE__*/_react.default.createElement("tr", {
         key: base
-      }, /*#__PURE__*/_react["default"].createElement("td", null, base.toUpperCase()), /*#__PURE__*/_react["default"].createElement("td", null, score.total), /*#__PURE__*/_react["default"].createElement("td", null, base === 'total' || base === 'skip' ? '---' : "".concat(Math.floor(score.total / (total || score.total || 1) * 100), "%")), /*#__PURE__*/_react["default"].createElement("td", null, strands['-1'] ? "".concat(strands['-1'], "(-)") : '', strands['1'] ? "".concat(strands['1'], "(+)") : ''), /*#__PURE__*/_react["default"].createElement("td", null, key));
+      }, /*#__PURE__*/_react.default.createElement("td", null, base.toUpperCase()), /*#__PURE__*/_react.default.createElement("td", null, score.total), /*#__PURE__*/_react.default.createElement("td", null, base === 'total' || base === 'skip' ? '---' : "".concat(Math.floor(score.total / (total || score.total || 1) * 100), "%")), /*#__PURE__*/_react.default.createElement("td", null, strands['-1'] ? "".concat(strands['-1'], "(-)") : '', strands['1'] ? "".concat(strands['1'], "(+)") : ''), /*#__PURE__*/_react.default.createElement("td", null, key));
     });
   }))));
 });
@@ -55,9 +55,9 @@ var TooltipContents = /*#__PURE__*/_react["default"].forwardRef(function (_ref,
 var SNPCoverageTooltip = (0, _mobxReact.observer)(function (props) {
   var model = props.model;
   var feat = model.featureUnderMouse;
-  return feat && feat.get('type') === 'skip' ? null : /*#__PURE__*/_react["default"].createElement(_pluginWiggle.Tooltip, (0, _extends2["default"])({
+  return feat && feat.get('type') === 'skip' ? null : /*#__PURE__*/_react.default.createElement(_pluginWiggle.Tooltip, (0, _extends2.default)({
     TooltipContents: TooltipContents
   }, props));
 });
 var _default = SNPCoverageTooltip;
-exports["default"] = _default;
+exports.default = _default;

package/dist/LinearSNPCoverageDisplay/index.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = register;
+exports.default = register;
 
 var _configSchema = _interopRequireDefault(require("./models/configSchema"));
 
@@ -17,11 +17,11 @@ var _DisplayType = _interopRequireDefault(require("@jbrowse/core/pluggableElemen
 
 function register(pluginManager) {
   pluginManager.addDisplayType(function () {
-    var configSchema = (0, _configSchema["default"])(pluginManager);
-    return new _DisplayType["default"]({
+    var configSchema = (0, _configSchema.default)(pluginManager);
+    return new _DisplayType.default({
       name: 'LinearSNPCoverageDisplay',
       configSchema: configSchema,
-      stateModel: (0, _model["default"])(pluginManager, configSchema),
+      stateModel: (0, _model.default)(pluginManager, configSchema),
       trackType: 'AlignmentsTrack',
       viewType: 'LinearGenomeView',
       ReactComponent: _pluginWiggle.LinearWiggleDisplayReactComponent

package/dist/LinearSNPCoverageDisplay/models/configSchema.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = SNPCoverageConfigFactory;
+exports.default = SNPCoverageConfigFactory;
 
 var _configuration = require("@jbrowse/core/configuration");
 

package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js

@@ -20,7 +20,7 @@ var _SNPCoverageRenderer = _interopRequireDefault(require("../../SNPCoverageRend
 
 var _configSchema = _interopRequireDefault(require("./configSchema"));
 
-function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2["default"])(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2["default"])(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2["default"])(this, result); }; }
+function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
 
 function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
 
@@ -33,26 +33,26 @@ afterEach(function () {
 }); // change renderer
 
 var SNPCoverageRendererPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2["default"])(SNPCoverageRendererPlugin, _Plugin);
+  (0, _inherits2.default)(SNPCoverageRendererPlugin, _Plugin);
 
   var _super = _createSuper(SNPCoverageRendererPlugin);
 
   function SNPCoverageRendererPlugin() {
-    (0, _classCallCheck2["default"])(this, SNPCoverageRendererPlugin);
+    (0, _classCallCheck2.default)(this, SNPCoverageRendererPlugin);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2["default"])(SNPCoverageRendererPlugin, [{
+  (0, _createClass2.default)(SNPCoverageRendererPlugin, [{
     key: "install",
     value: function install(pluginManager) {
-      (0, _SNPCoverageRenderer["default"])(pluginManager);
+      (0, _SNPCoverageRenderer.default)(pluginManager);
     }
   }]);
   return SNPCoverageRendererPlugin;
-}(_Plugin2["default"]);
+}(_Plugin2.default);
 
 test('has a type attr', function () {
-  var configSchema = (0, _configSchema["default"])(new _PluginManager["default"]([new SNPCoverageRendererPlugin()]).createPluggableElements().configure());
+  var configSchema = (0, _configSchema.default)(new _PluginManager.default([new SNPCoverageRendererPlugin()]).createPluggableElements().configure());
   var config = configSchema.create({
     type: 'LinearSNPCoverageDisplay',
     displayId: 'display1',

package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -177,7 +177,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         headers?: Record<string, string> | undefined;
         signal?: AbortSignal | undefined;
         filters?: string[] | undefined;
-    }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    }): Promise<{}>;
     setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
     setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
     clearRegionStats(): void;

package/dist/LinearSNPCoverageDisplay/models/model.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -31,7 +31,7 @@ var _shared = require("../../shared");
 
 function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
 
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
 
 // using a map because it preserves order
 var rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
@@ -39,9 +39,9 @@ var rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
 var stateModelFactory = function stateModelFactory(pluginManager, configSchema) {
   return _mobxStateTree.types.compose('LinearSNPCoverageDisplay', (0, _pluginWiggle.linearWiggleDisplayModelFactory)(pluginManager, configSchema), _mobxStateTree.types.model({
     type: _mobxStateTree.types.literal('LinearSNPCoverageDisplay'),
-    drawInterbaseCounts: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
-    drawIndicators: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
-    drawArcs: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
+    drawInterbaseCounts: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
+    drawIndicators: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
+    drawArcs: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
     filterBy: _mobxStateTree.types.optional(_mobxStateTree.types.model({
       flagInclude: _mobxStateTree.types.optional(_mobxStateTree.types.number, 0),
       flagExclude: _mobxStateTree.types.optional(_mobxStateTree.types.number, 1540),
@@ -55,7 +55,7 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
       type: _mobxStateTree.types.string,
       tag: _mobxStateTree.types.maybe(_mobxStateTree.types.string)
     }))
-  }))["volatile"](function () {
+  })).volatile(function () {
     return {
       modificationTagMap: _mobx.observable.map({})
     };
@@ -135,10 +135,10 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
         self.drawArcs = !self.drawArcsSetting;
       },
       afterAttach: function afterAttach() {
-        (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
           var colorBy, _ref2, staticBlocks, vals;
 
-          return _regenerator["default"].wrap(function _callee$(_context) {
+          return _regenerator.default.wrap(function _callee$(_context) {
             while (1) {
               switch (_context.prev = _context.next) {
                 case 0:
@@ -183,7 +183,7 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
     var superTrackMenuItems = self.trackMenuItems;
     return {
       get TooltipComponent() {
-        return _Tooltip["default"];
+        return _Tooltip.default;
       },
 
       get adapterConfig() {
@@ -206,7 +206,7 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
         return [];
       },
       trackMenuItems: function trackMenuItems() {
-        return [].concat((0, _toConsumableArray2["default"])(superTrackMenuItems()), [{
+        return [].concat((0, _toConsumableArray2.default)(superTrackMenuItems()), [{
           label: 'Draw insertion/clipping indicators',
           type: 'checkbox',
           checked: self.drawIndicatorsSetting,
@@ -234,4 +234,4 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
 };
 
 var _default = stateModelFactory;
-exports["default"] = _default;
+exports.default = _default;