@jbrowse/plugin-alignments 1.7.3 → 1.7.4

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.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 _react = _interopRequireDefault(require("react"));
 
@@ -35,16 +35,16 @@ function AlignmentsDisplay(_ref) {
       showCoverage = model.showCoverage;
   var classes = useStyles();
   var top = SNPCoverageDisplay.height;
-  return /*#__PURE__*/_react["default"].createElement("div", {
+  return /*#__PURE__*/_react.default.createElement("div", {
     "data-testid": "display-".concat((0, _configuration.getConf)(model, 'displayId')),
     style: {
       position: 'relative'
     }
-  }, showCoverage ? /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, /*#__PURE__*/_react["default"].createElement("div", {
+  }, showCoverage ? /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement("div", {
     "data-testid": "Blockset-snpcoverage"
-  }, /*#__PURE__*/_react["default"].createElement(SNPCoverageDisplay.RenderingComponent, {
+  }, /*#__PURE__*/_react.default.createElement(SNPCoverageDisplay.RenderingComponent, {
     model: SNPCoverageDisplay
-  })), /*#__PURE__*/_react["default"].createElement(_ui.ResizeHandle, {
+  })), /*#__PURE__*/_react.default.createElement(_ui.ResizeHandle, {
     onDrag: function onDrag(delta) {
       SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
       return delta;
@@ -53,17 +53,17 @@ function AlignmentsDisplay(_ref) {
     style: {
       top: top
     }
-  })) : null, showPileup ? /*#__PURE__*/_react["default"].createElement("div", {
+  })) : null, showPileup ? /*#__PURE__*/_react.default.createElement("div", {
     "data-testid": "Blockset-pileup",
     style: {
       position: 'absolute',
       top: showCoverage ? SNPCoverageDisplay.height : 0
     }
-  }, /*#__PURE__*/_react["default"].createElement(PileupDisplay.RenderingComponent, {
+  }, /*#__PURE__*/_react.default.createElement(PileupDisplay.RenderingComponent, {
     model: PileupDisplay
   })) : null);
 }
 
 var _default = (0, _mobxReact.observer)(AlignmentsDisplay);
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/LinearAlignmentsDisplay/index.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = _default;
+exports.default = _default;
 
 var _DisplayType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 
@@ -18,14 +18,14 @@ var _AlignmentsDisplay = _interopRequireDefault(require("./components/Alignments
 // locals
 function _default(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: 'LinearAlignmentsDisplay',
       configSchema: configSchema,
-      stateModel: (0, _model["default"])(pluginManager, configSchema),
+      stateModel: (0, _model.default)(pluginManager, configSchema),
       trackType: 'AlignmentsTrack',
       viewType: 'LinearGenomeView',
-      ReactComponent: _AlignmentsDisplay["default"]
+      ReactComponent: _AlignmentsDisplay.default
     });
   });
 }

package/dist/LinearAlignmentsDisplay/models/configSchema.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _configuration = require("@jbrowse/core/configuration");
 
@@ -22,4 +22,4 @@ var configModelFactory = function configModelFactory(pluginManager) {
 };
 
 var _default = configModelFactory;
-exports["default"] = _default;
+exports.default = _default;

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

@@ -30,7 +30,7 @@ var _LinearSNPCoverageDisplay = _interopRequireDefault(require("../../LinearSNPC
 
 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; } }
 
@@ -43,37 +43,37 @@ afterEach(function () {
 });
 
 var AlignmentsPlugin = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2["default"])(AlignmentsPlugin, _Plugin);
+  (0, _inherits2.default)(AlignmentsPlugin, _Plugin);
 
   var _super = _createSuper(AlignmentsPlugin);
 
   function AlignmentsPlugin() {
-    (0, _classCallCheck2["default"])(this, AlignmentsPlugin);
+    (0, _classCallCheck2.default)(this, AlignmentsPlugin);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2["default"])(AlignmentsPlugin, [{
+  (0, _createClass2.default)(AlignmentsPlugin, [{
     key: "install",
     value: function install(pluginManager) {
-      (0, _PileupRenderer["default"])(pluginManager);
+      (0, _PileupRenderer.default)(pluginManager);
       pluginManager.addRendererType(function () {
-        return new _BoxRendererType["default"]({
+        return new _BoxRendererType.default({
           name: 'SvgFeatureRenderer',
           ReactComponent: _pluginSvg.SvgFeatureRendererReactComponent,
           configSchema: _pluginSvg.svgFeatureRendererConfigSchema,
           pluginManager: pluginManager
         });
       });
-      (0, _SNPCoverageRenderer["default"])(pluginManager);
-      (0, _LinearPileupDisplay["default"])(pluginManager);
-      (0, _LinearSNPCoverageDisplay["default"])(pluginManager);
+      (0, _SNPCoverageRenderer.default)(pluginManager);
+      (0, _LinearPileupDisplay.default)(pluginManager);
+      (0, _LinearSNPCoverageDisplay.default)(pluginManager);
     }
   }]);
   return AlignmentsPlugin;
-}(_Plugin2["default"]);
+}(_Plugin2.default);
 
 test('has a type attr', function () {
-  var configSchema = (0, _configSchema["default"])(new _PluginManager["default"]([new AlignmentsPlugin()]).createPluggableElements().configure());
+  var configSchema = (0, _configSchema.default)(new _PluginManager.default([new AlignmentsPlugin()]).createPluggableElements().configure());
   var config = configSchema.create({
     type: 'LinearAlignmentsDisplay',
     displayId: 'display0',

package/dist/LinearAlignmentsDisplay/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 _fastDeepEqual = _interopRequireDefault(require("fast-deep-equal"));
 
 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; }
 
 var minDisplayHeight = 20;
 
@@ -46,7 +46,7 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
     showCoverage: true,
     showPileup: true,
     userFeatureScreenDensity: _mobxStateTree.types.maybe(_mobxStateTree.types.number)
-  }))["volatile"](function () {
+  })).volatile(function () {
     return {
       scrollTop: 0
     };
@@ -120,7 +120,7 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
       },
 
       trackMenuItems: function trackMenuItems() {
-        return [].concat((0, _toConsumableArray2["default"])(superTrackMenuItems()), [{
+        return [].concat((0, _toConsumableArray2.default)(superTrackMenuItems()), [{
           type: 'subMenu',
           label: 'Pileup settings',
           subMenu: self.PileupDisplay.trackMenuItems()
@@ -171,25 +171,25 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
         (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)(function () {
           if (!self.SNPCoverageDisplay) {
             self.setSNPCoverageDisplay(self.snpCoverageDisplayConfig);
-          } else if (!(0, _fastDeepEqual["default"])(self.snpCoverageDisplayConfig, (0, _mobxStateTree.getSnapshot)(self.SNPCoverageDisplay.configuration))) {
+          } else if (!(0, _fastDeepEqual.default)(self.snpCoverageDisplayConfig, (0, _mobxStateTree.getSnapshot)(self.SNPCoverageDisplay.configuration))) {
             self.SNPCoverageDisplay.setHeight(self.snpCovHeight);
             self.SNPCoverageDisplay.setConfig(self.snpCoverageDisplayConfig);
           }
 
           if (!self.PileupDisplay) {
             self.setPileupDisplay(self.pileupDisplayConfig);
-          } else if (!(0, _fastDeepEqual["default"])(self.pileupDisplayConfig, (0, _mobxStateTree.getSnapshot)(self.PileupDisplay.configuration))) {
+          } else if (!(0, _fastDeepEqual.default)(self.pileupDisplayConfig, (0, _mobxStateTree.getSnapshot)(self.PileupDisplay.configuration))) {
             self.PileupDisplay.setConfig(self.pileupDisplayConfig);
           } // propagate the filterBy setting from pileupdisplay to snpcoverage
           // note: the snpcoverage display is not able to control filterBy
           // itself
 
 
-          if (self.PileupDisplay.filterBy && !(0, _fastDeepEqual["default"])((0, _mobxStateTree.getSnapshot)(self.PileupDisplay.filterBy), (0, _mobxStateTree.getSnapshot)(self.SNPCoverageDisplay.filterBy))) {
+          if (self.PileupDisplay.filterBy && !(0, _fastDeepEqual.default)((0, _mobxStateTree.getSnapshot)(self.PileupDisplay.filterBy), (0, _mobxStateTree.getSnapshot)(self.SNPCoverageDisplay.filterBy))) {
             self.SNPCoverageDisplay.setFilterBy((0, _mobxStateTree.getSnapshot)(self.PileupDisplay.filterBy));
           }
 
-          if (self.PileupDisplay.colorBy && !(0, _fastDeepEqual["default"])((0, _mobxStateTree.getSnapshot)(self.PileupDisplay.colorBy), self.SNPCoverageDisplay.colorBy ? (0, _mobxStateTree.getSnapshot)(self.SNPCoverageDisplay.colorBy) : {})) {
+          if (self.PileupDisplay.colorBy && !(0, _fastDeepEqual.default)((0, _mobxStateTree.getSnapshot)(self.PileupDisplay.colorBy), self.SNPCoverageDisplay.colorBy ? (0, _mobxStateTree.getSnapshot)(self.SNPCoverageDisplay.colorBy) : {})) {
             self.SNPCoverageDisplay.setColorBy((0, _mobxStateTree.getSnapshot)(self.PileupDisplay.colorBy));
           }
         }));
@@ -198,9 +198,9 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
         }));
       },
       renderSvg: function renderSvg(opts) {
-        return (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
           var pileupHeight;
-          return _regenerator["default"].wrap(function _callee$(_context) {
+          return _regenerator.default.wrap(function _callee$(_context) {
             while (1) {
               switch (_context.prev = _context.next) {
                 case 0:
@@ -211,16 +211,16 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
                   });
 
                 case 3:
-                  _context.t0 = _react["default"];
-                  _context.t1 = _react["default"].Fragment;
-                  _context.t2 = _react["default"];
+                  _context.t0 = _react.default;
+                  _context.t1 = _react.default.Fragment;
+                  _context.t2 = _react.default;
                   _context.next = 8;
                   return self.SNPCoverageDisplay.renderSvg(opts);
 
                 case 8:
                   _context.t3 = _context.sent;
                   _context.t4 = _context.t2.createElement.call(_context.t2, "g", null, _context.t3);
-                  _context.t5 = _react["default"];
+                  _context.t5 = _react.default;
                   _context.t6 = {
                     transform: "translate(0 ".concat(self.SNPCoverageDisplay.height, ")")
                   };
@@ -247,4 +247,4 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
 };
 
 var _default = stateModelFactory;
-exports["default"] = _default;
+exports.default = _default;

package/dist/LinearPileupDisplay/components/ColorByModifications.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 _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
@@ -40,16 +40,16 @@ var useStyles = (0, _core.makeStyles)(function (theme) {
 function ModificationTable(_ref) {
   var modifications = _ref.modifications;
   var classes = useStyles();
-  return /*#__PURE__*/_react["default"].createElement("table", {
+  return /*#__PURE__*/_react.default.createElement("table", {
     className: classes.table
-  }, /*#__PURE__*/_react["default"].createElement("tbody", null, modifications.map(function (_ref2) {
-    var _ref3 = (0, _slicedToArray2["default"])(_ref2, 2),
+  }, /*#__PURE__*/_react.default.createElement("tbody", null, modifications.map(function (_ref2) {
+    var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
         key = _ref3[0],
         value = _ref3[1];
 
-    return /*#__PURE__*/_react["default"].createElement("tr", {
+    return /*#__PURE__*/_react.default.createElement("tr", {
       key: key
-    }, /*#__PURE__*/_react["default"].createElement("td", null, key), /*#__PURE__*/_react["default"].createElement("td", null, value), /*#__PURE__*/_react["default"].createElement("td", {
+    }, /*#__PURE__*/_react.default.createElement("td", null, key), /*#__PURE__*/_react.default.createElement("td", null, value), /*#__PURE__*/_react.default.createElement("td", {
       style: {
         width: '1em',
         background: value
@@ -64,25 +64,25 @@ function ColorByTagDlg(props) {
       handleClose = props.handleClose;
   var colorBy = model.colorBy,
       modificationTagMap = model.modificationTagMap;
-  var modifications = (0, _toConsumableArray2["default"])(modificationTagMap.entries());
-  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+  var modifications = (0, _toConsumableArray2.default)(modificationTagMap.entries());
+  return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
     open: true,
     onClose: handleClose
-  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Color by modifications", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+  }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, null, "Color by modifications", /*#__PURE__*/_react.default.createElement(_core.IconButton, {
     "aria-label": "close",
     className: classes.closeButton,
     onClick: handleClose
-  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "You can choose to color the modifications in the BAM/CRAM MM/ML specification using this dialog. Choosing modifications colors the modified positions and can color multiple modification types. Choosing the methylation setting colors methylated and unmethylated CpG."), /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Note: you can revisit this dialog to see the current mapping of colors to modification type for the modification coloring mode"), /*#__PURE__*/_react["default"].createElement("div", {
+  }, /*#__PURE__*/_react.default.createElement(_Close.default, null))), /*#__PURE__*/_react.default.createElement(_core.DialogContent, null, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "You can choose to color the modifications in the BAM/CRAM MM/ML specification using this dialog. Choosing modifications colors the modified positions and can color multiple modification types. Choosing the methylation setting colors methylated and unmethylated CpG."), /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Note: you can revisit this dialog to see the current mapping of colors to modification type for the modification coloring mode"), /*#__PURE__*/_react.default.createElement("div", {
     style: {
       margin: 20
     }
-  }, (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications' ? /*#__PURE__*/_react["default"].createElement("div", null, modifications.length ? /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, "Current modification-type-to-color mapping", /*#__PURE__*/_react["default"].createElement(ModificationTable, {
-    modifications: (0, _toConsumableArray2["default"])(modificationTagMap.entries())
-  })) : /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Note: color by modifications is already enabled. Loading current modifications..."), /*#__PURE__*/_react["default"].createElement(_core.CircularProgress, {
+  }, (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications' ? /*#__PURE__*/_react.default.createElement("div", null, modifications.length ? /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, "Current modification-type-to-color mapping", /*#__PURE__*/_react.default.createElement(ModificationTable, {
+    modifications: (0, _toConsumableArray2.default)(modificationTagMap.entries())
+  })) : /*#__PURE__*/_react.default.createElement("div", null, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Note: color by modifications is already enabled. Loading current modifications..."), /*#__PURE__*/_react.default.createElement(_core.CircularProgress, {
     size: 15
-  }))) : null, (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' ? /*#__PURE__*/_react["default"].createElement(ModificationTable, {
+  }))) : null, (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation' ? /*#__PURE__*/_react.default.createElement(ModificationTable, {
     modifications: [['methylated', 'red'], ['unmethylated', 'blue']]
-  }) : null), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+  }) : null), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
     variant: "contained",
     color: "primary",
     style: {
@@ -94,7 +94,7 @@ function ColorByTagDlg(props) {
       });
       handleClose();
     }
-  }, "Modifications"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+  }, "Modifications"), /*#__PURE__*/_react.default.createElement(_core.Button, {
     variant: "contained",
     color: "primary",
     style: {
@@ -106,7 +106,7 @@ function ColorByTagDlg(props) {
       });
       handleClose();
     }
-  }, "Methylation"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+  }, "Methylation"), /*#__PURE__*/_react.default.createElement(_core.Button, {
     variant: "contained",
     color: "secondary",
     style: {
@@ -120,4 +120,4 @@ function ColorByTagDlg(props) {
 
 var _default = (0, _mobxReact.observer)(ColorByTagDlg);
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/LinearPileupDisplay/components/ColorByTag.js

@@ -7,7 +7,7 @@ var _typeof = require("@babel/runtime/helpers/typeof");
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
@@ -21,7 +21,7 @@ var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
 
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
 var useStyles = (0, _core.makeStyles)(function (theme) {
   return {
@@ -43,25 +43,25 @@ function ColorByTagDlg(props) {
       handleClose = props.handleClose;
 
   var _useState = (0, _react.useState)(''),
-      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
       tag = _useState2[0],
       setTag = _useState2[1];
 
   var validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
-  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+  return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
     open: true,
     onClose: handleClose
-  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Color by tag", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+  }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, null, "Color by tag", /*#__PURE__*/_react.default.createElement(_core.IconButton, {
     "aria-label": "close",
     className: classes.closeButton,
     onClick: handleClose
-  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, {
+  }, /*#__PURE__*/_react.default.createElement(_Close.default, null))), /*#__PURE__*/_react.default.createElement(_core.DialogContent, {
     style: {
       overflowX: 'hidden'
     }
-  }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Enter tag to color by: "), /*#__PURE__*/_react["default"].createElement(_core.Typography, {
+  }, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Enter tag to color by: "), /*#__PURE__*/_react.default.createElement(_core.Typography, {
     color: "textSecondary"
-  }, "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+  }, "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."), /*#__PURE__*/_react.default.createElement(_core.TextField, {
     value: tag,
     onChange: function onChange(event) {
       return setTag(event.target.value);
@@ -75,7 +75,7 @@ function ColorByTagDlg(props) {
     helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '',
     autoComplete: "off",
     "data-testid": "color-tag-name"
-  }), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+  }), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
     variant: "contained",
     color: "primary",
     onClick: function onClick() {
@@ -86,7 +86,7 @@ function ColorByTagDlg(props) {
       handleClose();
     },
     disabled: !validTag
-  }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+  }, "Submit"), /*#__PURE__*/_react.default.createElement(_core.Button, {
     variant: "contained",
     color: "secondary",
     onClick: handleClose
@@ -95,4 +95,4 @@ function ColorByTagDlg(props) {
 
 var _default = (0, _mobxReact.observer)(ColorByTagDlg);
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/LinearPileupDisplay/components/FilterByTag.js

@@ -7,7 +7,7 @@ var _typeof = require("@babel/runtime/helpers/typeof");
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
 
@@ -21,7 +21,7 @@ var _Close = _interopRequireDefault(require("@material-ui/icons/Close"));
 
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
 var useStyles = (0, _core.makeStyles)(function (theme) {
   return {
@@ -46,7 +46,7 @@ function Bitmask(props) {
   var _props$flag = props.flag,
       flag = _props$flag === void 0 ? 0 : _props$flag,
       setFlag = props.setFlag;
-  return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement(_core.TextField, {
     type: "number",
     value: flag,
     onChange: function onChange(event) {
@@ -55,9 +55,9 @@ function Bitmask(props) {
   }), flagNames.map(function (name, index) {
     var val = flag & 1 << index;
     var key = "".concat(name, "_").concat(val);
-    return /*#__PURE__*/_react["default"].createElement("div", {
+    return /*#__PURE__*/_react.default.createElement("div", {
       key: key
-    }, /*#__PURE__*/_react["default"].createElement("input", {
+    }, /*#__PURE__*/_react.default.createElement("input", {
       type: "checkbox",
       checked: Boolean(val),
       onChange: function onChange(event) {
@@ -67,7 +67,7 @@ function Bitmask(props) {
           setFlag(flag & ~(1 << index));
         }
       }
-    }), /*#__PURE__*/_react["default"].createElement("label", {
+    }), /*#__PURE__*/_react.default.createElement("label", {
       htmlFor: key
     }, name));
   }));
@@ -82,58 +82,58 @@ function FilterByTagDlg(props) {
   var filterBy = model.filterBy;
 
   var _useState = (0, _react.useState)(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagInclude),
-      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
       flagInclude = _useState2[0],
       setFlagInclude = _useState2[1];
 
   var _useState3 = (0, _react.useState)(filterBy === null || filterBy === void 0 ? void 0 : filterBy.flagExclude),
-      _useState4 = (0, _slicedToArray2["default"])(_useState3, 2),
+      _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
       flagExclude = _useState4[0],
       setFlagExclude = _useState4[1];
 
   var _useState5 = (0, _react.useState)((filterBy === null || filterBy === void 0 ? void 0 : (_filterBy$tagFilter = filterBy.tagFilter) === null || _filterBy$tagFilter === void 0 ? void 0 : _filterBy$tagFilter.tag) || ''),
-      _useState6 = (0, _slicedToArray2["default"])(_useState5, 2),
+      _useState6 = (0, _slicedToArray2.default)(_useState5, 2),
       tag = _useState6[0],
       setTag = _useState6[1];
 
   var _useState7 = (0, _react.useState)((filterBy === null || filterBy === void 0 ? void 0 : (_filterBy$tagFilter2 = filterBy.tagFilter) === null || _filterBy$tagFilter2 === void 0 ? void 0 : _filterBy$tagFilter2.value) || ''),
-      _useState8 = (0, _slicedToArray2["default"])(_useState7, 2),
+      _useState8 = (0, _slicedToArray2.default)(_useState7, 2),
       tagValue = _useState8[0],
       setTagValue = _useState8[1];
 
   var _useState9 = (0, _react.useState)((filterBy === null || filterBy === void 0 ? void 0 : filterBy.readName) || ''),
-      _useState10 = (0, _slicedToArray2["default"])(_useState9, 2),
+      _useState10 = (0, _slicedToArray2.default)(_useState9, 2),
       readName = _useState10[0],
       setReadName = _useState10[1];
 
   var validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/);
   var site = 'https://broadinstitute.github.io/picard/explain-flags.html';
-  return /*#__PURE__*/_react["default"].createElement(_core.Dialog, {
+  return /*#__PURE__*/_react.default.createElement(_core.Dialog, {
     open: true,
     onClose: handleClose
-  }, /*#__PURE__*/_react["default"].createElement(_core.DialogTitle, null, "Filter options", /*#__PURE__*/_react["default"].createElement(_core.IconButton, {
+  }, /*#__PURE__*/_react.default.createElement(_core.DialogTitle, null, "Filter options", /*#__PURE__*/_react.default.createElement(_core.IconButton, {
     "aria-label": "close",
     className: classes.closeButton,
     onClick: handleClose
-  }, /*#__PURE__*/_react["default"].createElement(_Close["default"], null))), /*#__PURE__*/_react["default"].createElement(_core.DialogContent, null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Set filter bitmask options. Refer to ", /*#__PURE__*/_react["default"].createElement(_core.Link, {
+  }, /*#__PURE__*/_react.default.createElement(_Close.default, null))), /*#__PURE__*/_react.default.createElement(_core.DialogContent, null, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Set filter bitmask options. Refer to ", /*#__PURE__*/_react.default.createElement(_core.Link, {
     href: site
-  }, site), ' ', "for details"), /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+  }, site), ' ', "for details"), /*#__PURE__*/_react.default.createElement(_core.Paper, {
     className: classes.paper,
     variant: "outlined"
-  }, /*#__PURE__*/_react["default"].createElement("div", {
+  }, /*#__PURE__*/_react.default.createElement("div", {
     style: {
       display: 'flex'
     }
-  }, /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Read must have ALL these flags"), /*#__PURE__*/_react["default"].createElement(Bitmask, {
+  }, /*#__PURE__*/_react.default.createElement("div", null, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Read must have ALL these flags"), /*#__PURE__*/_react.default.createElement(Bitmask, {
     flag: flagInclude,
     setFlag: setFlagInclude
-  })), /*#__PURE__*/_react["default"].createElement("div", null, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Read must have NONE of these flags"), /*#__PURE__*/_react["default"].createElement(Bitmask, {
+  })), /*#__PURE__*/_react.default.createElement("div", null, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Read must have NONE of these flags"), /*#__PURE__*/_react.default.createElement(Bitmask, {
     flag: flagExclude,
     setFlag: setFlagExclude
-  })))), /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+  })))), /*#__PURE__*/_react.default.createElement(_core.Paper, {
     className: classes.paper,
     variant: "outlined"
-  }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+  }, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"), /*#__PURE__*/_react.default.createElement(_core.TextField, {
     className: classes.field,
     value: tag,
     onChange: function onChange(event) {
@@ -147,7 +147,7 @@ function FilterByTagDlg(props) {
     error: tag.length === 2 && !validTag,
     helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '',
     "data-testid": "color-tag-name"
-  }), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+  }), /*#__PURE__*/_react.default.createElement(_core.TextField, {
     className: classes.field,
     value: tagValue,
     onChange: function onChange(event) {
@@ -158,10 +158,10 @@ function FilterByTagDlg(props) {
       'data-testid': 'color-tag-name-input'
     },
     "data-testid": "color-tag-value"
-  })), /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+  })), /*#__PURE__*/_react.default.createElement(_core.Paper, {
     className: classes.paper,
     variant: "outlined"
-  }, /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "Filter by read name"), /*#__PURE__*/_react["default"].createElement(_core.TextField, {
+  }, /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Filter by read name"), /*#__PURE__*/_react.default.createElement(_core.TextField, {
     className: classes.field,
     value: readName,
     onChange: function onChange(event) {
@@ -172,7 +172,7 @@ function FilterByTagDlg(props) {
       'data-testid': 'color-tag-readname-input'
     },
     "data-testid": "color-tag-readname"
-  })), /*#__PURE__*/_react["default"].createElement(_core.DialogActions, null, /*#__PURE__*/_react["default"].createElement(_core.Button, {
+  })), /*#__PURE__*/_react.default.createElement(_core.DialogActions, null, /*#__PURE__*/_react.default.createElement(_core.Button, {
     variant: "contained",
     color: "primary",
     autoFocus: true,
@@ -189,7 +189,7 @@ function FilterByTagDlg(props) {
       });
       handleClose();
     }
-  }, "Submit"), /*#__PURE__*/_react["default"].createElement(_core.Button, {
+  }, "Submit"), /*#__PURE__*/_react.default.createElement(_core.Button, {
     variant: "contained",
     color: "secondary",
     onClick: function onClick() {
@@ -200,4 +200,4 @@ function FilterByTagDlg(props) {
 
 var _default = (0, _mobxReact.observer)(FilterByTagDlg);
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.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 _react = _interopRequireDefault(require("react"));
 
@@ -16,12 +16,12 @@ var _Typography = _interopRequireDefault(require("@material-ui/core/Typography")
 function LinearPileupDisplayBlurb(props) {
   var model = props.model;
   var sortedBy = model.sortedBy;
-  return sortedBy ? /*#__PURE__*/_react["default"].createElement("div", {
+  return sortedBy ? /*#__PURE__*/_react.default.createElement("div", {
     "data-testid": "blurb-".concat(model.sortedBy),
     style: {
       backgroundColor: 'white'
     }
-  }, /*#__PURE__*/_react["default"].createElement(_Typography["default"], {
+  }, /*#__PURE__*/_react.default.createElement(_Typography.default, {
     color: "secondary",
     variant: "caption"
   }, model.sortedBy ? "Sorted by ".concat(sortedBy.type.toLowerCase(), " at ").concat(sortedBy.refName, ":").concat(sortedBy.pos) : null)) : null;
@@ -29,4 +29,4 @@ function LinearPileupDisplayBlurb(props) {
 
 var _default = (0, _mobxReact.observer)(LinearPileupDisplayBlurb);
 
-exports["default"] = _default;
+exports.default = _default;