@jbrowse/plugin-alignments 1.7.3 → 1.7.6

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.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"));
 
@@ -29,7 +29,7 @@ var _MismatchParser = require("../BamAdapter/MismatchParser");
 
 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 () {
   return {
@@ -47,17 +47,17 @@ function AlignmentFlags(props) {
   var feature = props.feature;
   var flags = feature.flags;
   var flagNames = ['read paired', 'read mapped in proper pair', 'read unmapped', 'mate unmapped', 'read reverse strand', 'mate reverse strand', 'first in pair', 'second in pair', 'not primary alignment', 'read fails platform/vendor quality checks', 'read is PCR or optical duplicate', 'supplementary alignment'];
-  return /*#__PURE__*/_react["default"].createElement(_BaseFeatureDetail.BaseCard, (0, _extends2["default"])({}, props, {
+  return /*#__PURE__*/_react.default.createElement(_BaseFeatureDetail.BaseCard, (0, _extends2.default)({}, props, {
     title: "Flags"
-  }), /*#__PURE__*/_react["default"].createElement(_BaseFeatureDetail.SimpleValue, {
+  }), /*#__PURE__*/_react.default.createElement(_BaseFeatureDetail.SimpleValue, {
     name: 'Flag',
     value: flags
-  }), /*#__PURE__*/_react["default"].createElement(_core.FormGroup, null, flagNames.map(function (name, index) {
+  }), /*#__PURE__*/_react.default.createElement(_core.FormGroup, null, flagNames.map(function (name, index) {
     var val = flags & 1 << index;
     var key = "".concat(name, "_").concat(val);
-    return /*#__PURE__*/_react["default"].createElement(_core.FormControlLabel, {
+    return /*#__PURE__*/_react.default.createElement(_core.FormControlLabel, {
       key: key,
-      control: /*#__PURE__*/_react["default"].createElement(_core.Checkbox, {
+      control: /*#__PURE__*/_react.default.createElement(_core.Checkbox, {
         className: classes.compact,
         checked: Boolean(val),
         name: name,
@@ -72,29 +72,29 @@ function Formatter(_ref) {
   var value = _ref.value;
 
   var _useState = (0, _react.useState)(false),
-      _useState2 = (0, _slicedToArray2["default"])(_useState, 2),
+      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
       show = _useState2[0],
       setShow = _useState2[1];
 
   var display = String(value);
 
   if (display.length > 100) {
-    return /*#__PURE__*/_react["default"].createElement(_react["default"].Fragment, null, /*#__PURE__*/_react["default"].createElement("button", {
+    return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, /*#__PURE__*/_react.default.createElement("button", {
       type: "button",
       onClick: function onClick() {
-        return (0, _copyToClipboard["default"])(display);
+        return (0, _copyToClipboard.default)(display);
       }
-    }, "Copy"), /*#__PURE__*/_react["default"].createElement("button", {
+    }, "Copy"), /*#__PURE__*/_react.default.createElement("button", {
       type: "button",
       onClick: function onClick() {
         return setShow(function (val) {
           return !val;
         });
       }
-    }, show ? 'Show less' : 'Show more'), /*#__PURE__*/_react["default"].createElement("div", null, show ? display : "".concat(display.slice(0, 100), "...")));
+    }, show ? 'Show less' : 'Show more'), /*#__PURE__*/_react.default.createElement("div", null, show ? display : "".concat(display.slice(0, 100), "...")));
   }
 
-  return /*#__PURE__*/_react["default"].createElement("div", null, display);
+  return /*#__PURE__*/_react.default.createElement("div", null, display);
 } // utility function to get length of alignment from cigar
 
 
@@ -119,13 +119,13 @@ function SupplementaryAlignments(props) {
   var tag = props.tag,
       model = props.model;
   var session = (0, _util.getSession)(model);
-  return /*#__PURE__*/_react["default"].createElement(_BaseFeatureDetail.BaseCard, (0, _extends2["default"])({}, props, {
+  return /*#__PURE__*/_react.default.createElement(_BaseFeatureDetail.BaseCard, (0, _extends2.default)({}, props, {
     title: "Supplementary alignments"
-  }), /*#__PURE__*/_react["default"].createElement(_core.Typography, null, "List of supplementary alignment locations"), /*#__PURE__*/_react["default"].createElement("ul", null, tag.split(';').filter(function (SA) {
+  }), /*#__PURE__*/_react.default.createElement(_core.Typography, null, "List of supplementary alignment locations"), /*#__PURE__*/_react.default.createElement("ul", null, tag.split(';').filter(function (SA) {
     return !!SA;
   }).map(function (SA, index) {
     var _SA$split = SA.split(','),
-        _SA$split2 = (0, _slicedToArray2["default"])(_SA$split, 4),
+        _SA$split2 = (0, _slicedToArray2.default)(_SA$split, 4),
         saRef = _SA$split2[0],
         saStart = _SA$split2[1],
         saStrand = _SA$split2[2],
@@ -139,9 +139,9 @@ function SupplementaryAlignments(props) {
     var displayStart = start.toLocaleString('en-US');
     var displayEnd = end.toLocaleString('en-US');
     var displayString = "".concat(saRef, ":").concat(displayStart, "-").concat(displayEnd, " (").concat(saStrand, ")");
-    return /*#__PURE__*/_react["default"].createElement("li", {
+    return /*#__PURE__*/_react.default.createElement("li", {
       key: "".concat(locString, "-").concat(index)
-    }, /*#__PURE__*/_react["default"].createElement(_core.Link, {
+    }, /*#__PURE__*/_react.default.createElement(_core.Link, {
       onClick: function onClick() {
         var view = model.view;
 
@@ -166,7 +166,7 @@ function PairLink(_ref2) {
   var locString = _ref2.locString,
       model = _ref2.model;
   var session = (0, _util.getSession)(model);
-  return /*#__PURE__*/_react["default"].createElement(_core.Link, {
+  return /*#__PURE__*/_react.default.createElement(_core.Link, {
     onClick: function onClick() {
       var view = model.view;
 
@@ -190,27 +190,27 @@ function AlignmentFeatureDetails(props) {
   var model = props.model;
   var feat = JSON.parse(JSON.stringify(model.featureData));
   var SA = feat.tags && feat.tags.SA || feat.SA;
-  return /*#__PURE__*/_react["default"].createElement(_core.Paper, {
+  return /*#__PURE__*/_react.default.createElement(_core.Paper, {
     "data-testid": "alignment-side-drawer"
-  }, /*#__PURE__*/_react["default"].createElement(_BaseFeatureDetail.FeatureDetails, (0, _extends2["default"])({}, props, {
+  }, /*#__PURE__*/_react.default.createElement(_BaseFeatureDetail.FeatureDetails, (0, _extends2.default)({}, props, {
     omit: omit,
     feature: feat,
     formatter: function formatter(value, key) {
-      return key === 'next_segment_position' ? /*#__PURE__*/_react["default"].createElement(PairLink, {
+      return key === 'next_segment_position' ? /*#__PURE__*/_react.default.createElement(PairLink, {
         model: model,
         locString: value
-      }) : /*#__PURE__*/_react["default"].createElement(Formatter, {
+      }) : /*#__PURE__*/_react.default.createElement(Formatter, {
         value: value
       });
     }
-  })), SA ? /*#__PURE__*/_react["default"].createElement(SupplementaryAlignments, {
+  })), SA ? /*#__PURE__*/_react.default.createElement(SupplementaryAlignments, {
     model: model,
     tag: SA
-  }) : null, /*#__PURE__*/_react["default"].createElement(AlignmentFlags, (0, _extends2["default"])({
+  }) : null, /*#__PURE__*/_react.default.createElement(AlignmentFlags, (0, _extends2.default)({
     feature: feat
   }, props)));
 }
 
 var _default = (0, _mobxReact.observer)(AlignmentFeatureDetails);
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/AlignmentsFeatureDetail/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.configSchema = void 0;
-exports["default"] = register;
+exports.default = register;
 exports.stateModelFactory = stateModelFactory;
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
@@ -23,7 +23,7 @@ var _WidgetType = _interopRequireDefault(require("@jbrowse/core/pluggableElement
 
 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 configSchema = (0, _configuration.ConfigurationSchema)('AlignmentsFeatureWidget', {});
 exports.configSchema = configSchema;
@@ -48,7 +48,7 @@ function stateModelFactory(pluginManager) {
 
 function register(pluginManager) {
   pluginManager.addWidgetType(function () {
-    return new _WidgetType["default"]({
+    return new _WidgetType.default({
       name: 'AlignmentsFeatureWidget',
       heading: 'Feature details',
       configSchema: configSchema,

package/dist/AlignmentsFeatureDetail/index.test.js

@@ -18,7 +18,7 @@ var _AlignmentsFeatureDetail = _interopRequireDefault(require("./AlignmentsFeatu
 
 test('open up a widget', function () {
   console.warn = jest.fn();
-  var pluginManager = new _PluginManager["default"]([]);
+  var pluginManager = new _PluginManager.default([]);
 
   var Session = _mobxStateTree.types.model({
     pluginManager: _mobxStateTree.types.optional(_mobxStateTree.types.frozen(), {}),
@@ -49,7 +49,7 @@ test('open up a widget', function () {
     type: 'match'
   });
 
-  var _render = (0, _react.render)( /*#__PURE__*/_react2["default"].createElement(_AlignmentsFeatureDetail["default"], {
+  var _render = (0, _react.render)( /*#__PURE__*/_react2.default.createElement(_AlignmentsFeatureDetail.default, {
     model: session.widget
   })),
       container = _render.container,

package/dist/AlignmentsTrack/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 _TrackType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
 
@@ -22,7 +22,7 @@ function configSchemaFactory(pluginManager) {
 function register(pluginManager) {
   pluginManager.addTrackType(function () {
     var configSchema = configSchemaFactory(pluginManager);
-    var track = new _TrackType["default"]({
+    var track = new _TrackType.default({
       name: 'AlignmentsTrack',
       configSchema: configSchema,
       stateModel: (0, _models.createBaseTrackModel)(pluginManager, 'AlignmentsTrack', configSchema)

package/dist/BamAdapter/BamAdapter.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"));
 
@@ -43,45 +43,45 @@ var _configuration = require("@jbrowse/core/configuration");
 
 var _BamSlightlyLazyFeature = _interopRequireDefault(require("./BamSlightlyLazyFeature"));
 
-function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it["return"] != null) it["return"](); } finally { if (didErr) throw err; } } }; }
+function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
 
 function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
 
 function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
 
-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; } }
 
 var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2["default"])(BamAdapter, _BaseFeatureDataAdapt);
+  (0, _inherits2.default)(BamAdapter, _BaseFeatureDataAdapt);
 
   var _super = _createSuper(BamAdapter);
 
   function BamAdapter() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, BamAdapter);
+    (0, _classCallCheck2.default)(this, BamAdapter);
 
     for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
       args[_key] = arguments[_key];
     }
 
     _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "samHeader", void 0);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "setupP", void 0);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "configured", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "samHeader", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "setupP", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "configured", void 0);
     return _this;
   }
 
-  (0, _createClass2["default"])(BamAdapter, [{
+  (0, _createClass2.default)(BamAdapter, [{
     key: "configure",
     value: // derived classes may not use the same configuration so a custom
     // configure method allows derived classes to override this behavior
     function () {
-      var _configure = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+      var _configure = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
         var bamLocation, location, indexType, bam, adapterConfig;
-        return _regenerator["default"].wrap(function _callee$(_context) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -136,10 +136,10 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getHeader",
     value: function () {
-      var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(opts) {
+      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(opts) {
         var _yield$this$configure, bam;
 
-        return _regenerator["default"].wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -168,10 +168,10 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "setupPre",
     value: function () {
-      var _setupPre = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(opts) {
+      var _setupPre = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(opts) {
         var _ref2, _ref2$statusCallback, statusCallback, _yield$this$configure2, bam;
 
-        return _regenerator["default"].wrap(function _callee4$(_context4) {
+        return _regenerator.default.wrap(function _callee4$(_context4) {
           while (1) {
             switch (_context4.prev = _context4.next) {
               case 0:
@@ -183,9 +183,9 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 _yield$this$configure2 = _context4.sent;
                 bam = _yield$this$configure2.bam;
                 _context4.next = 7;
-                return (0, _util.updateStatus)('Downloading index', statusCallback, /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+                return (0, _util.updateStatus)('Downloading index', statusCallback, /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
                   var samHeader, idToName, nameToId;
-                  return _regenerator["default"].wrap(function _callee3$(_context3) {
+                  return _regenerator.default.wrap(function _callee3$(_context3) {
                     while (1) {
                       switch (_context3.prev = _context3.next) {
                         case 0:
@@ -244,15 +244,15 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "setup",
     value: function () {
-      var _setup = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5(opts) {
+      var _setup = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(opts) {
         var _this2 = this;
 
-        return _regenerator["default"].wrap(function _callee5$(_context5) {
+        return _regenerator.default.wrap(function _callee5$(_context5) {
           while (1) {
             switch (_context5.prev = _context5.next) {
               case 0:
                 if (!this.setupP) {
-                  this.setupP = this.setupPre(opts)["catch"](function (e) {
+                  this.setupP = this.setupPre(opts).catch(function (e) {
                     _this2.setupP = undefined;
                     throw e;
                   });
@@ -277,10 +277,10 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getRefNames",
     value: function () {
-      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee6(opts) {
+      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(opts) {
         var _yield$this$setup, idToName;
 
-        return _regenerator["default"].wrap(function _callee6$(_context6) {
+        return _regenerator.default.wrap(function _callee6$(_context6) {
           while (1) {
             switch (_context6.prev = _context6.next) {
               case 0:
@@ -309,10 +309,10 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "seqFetch",
     value: function () {
-      var _seqFetch = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee7(refName, start, end) {
+      var _seqFetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(refName, start, end) {
         var _yield$this$configure3, sequenceAdapter, refSeqStore, features, seqChunks, sequence;
 
-        return _regenerator["default"].wrap(function _callee7$(_context7) {
+        return _regenerator.default.wrap(function _callee7$(_context7) {
           while (1) {
             switch (_context7.prev = _context7.next) {
               case 0:
@@ -405,10 +405,10 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
           statusCallback = _ref4$statusCallback === void 0 ? function () {} : _ref4$statusCallback;
 
       return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref5 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee8(observer) {
+        var _ref5 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(observer) {
           var _yield$_this3$configu, bam, records, _ref6, _ref6$flagInclude, flagInclude, _ref6$flagExclude, flagExclude, tagFilter, name, _iterator, _step, record, ref, flags, val;
 
-          return _regenerator["default"].wrap(function _callee8$(_context8) {
+          return _regenerator.default.wrap(function _callee8$(_context8) {
             while (1) {
               switch (_context8.prev = _context8.next) {
                 case 0:
@@ -488,7 +488,7 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   return _context8.abrupt("continue", 31);
 
                 case 30:
-                  observer.next(new _BamSlightlyLazyFeature["default"](record, _this3, ref));
+                  observer.next(new _BamSlightlyLazyFeature.default(record, _this3, ref));
 
                 case 31:
                   _context8.next = 14;
@@ -531,10 +531,10 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "estimateRegionsStats",
     value: function () {
-      var _estimateRegionsStats = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee9(regions, opts) {
+      var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee9(regions, opts) {
         var _yield$this$configure4, bam, bytes, fetchSizeLimit;
 
-        return _regenerator["default"].wrap(function _callee9$(_context9) {
+        return _regenerator.default.wrap(function _callee9$(_context9) {
           while (1) {
             switch (_context9.prev = _context9.next) {
               case 0:
@@ -562,7 +562,7 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                 });
 
               case 12:
-                return _context9.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(BamAdapter.prototype), "estimateRegionsStats", this).call(this, regions, opts));
+                return _context9.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(BamAdapter.prototype), "estimateRegionsStats", this).call(this, regions, opts));
 
               case 13:
               case "end":
@@ -595,4 +595,4 @@ var BamAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   return BamAdapter;
 }(_BaseAdapter.BaseFeatureDataAdapter);
 
-exports["default"] = BamAdapter;
+exports.default = BamAdapter;

package/dist/BamAdapter/BamAdapter.test.js

@@ -12,13 +12,13 @@ var _BamAdapter = _interopRequireDefault(require("./BamAdapter"));
 
 var _configSchema = _interopRequireDefault(require("./configSchema"));
 
-test('adapter can fetch features from volvox.bam', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+test('adapter can fetch features from volvox.bam', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
   var adapter, features, featuresArray, featuresJsonArray, adapterCSI, featuresCSI, featuresArrayCSI, featuresJsonArrayCSI;
-  return _regenerator["default"].wrap(function _callee$(_context) {
+  return _regenerator.default.wrap(function _callee$(_context) {
     while (1) {
       switch (_context.prev = _context.next) {
         case 0:
-          adapter = new _BamAdapter["default"](_configSchema["default"].create({
+          adapter = new _BamAdapter.default(_configSchema.default.create({
             bamLocation: {
               localPath: require.resolve('../../test_data/volvox-sorted.bam'),
               locationType: 'LocalPathLocation'
@@ -56,7 +56,7 @@ test('adapter can fetch features from volvox.bam', /*#__PURE__*/(0, _asyncToGene
         case 14:
           _context.t1 = _context.sent;
           (0, _context.t0)(_context.t1).toBe(true);
-          adapterCSI = new _BamAdapter["default"](_configSchema["default"].create({
+          adapterCSI = new _BamAdapter.default(_configSchema.default.create({
             bamLocation: {
               localPath: require.resolve('../../test_data/volvox-sorted.bam'),
               locationType: 'LocalPathLocation'
@@ -92,13 +92,13 @@ test('adapter can fetch features from volvox.bam', /*#__PURE__*/(0, _asyncToGene
     }
   }, _callee);
 })));
-test('test usage of BamSlightlyLazyFeature toJSON (used in the widget)', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+test('test usage of BamSlightlyLazyFeature toJSON (used in the widget)', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
   var adapter, features, featuresArray, f;
-  return _regenerator["default"].wrap(function _callee2$(_context2) {
+  return _regenerator.default.wrap(function _callee2$(_context2) {
     while (1) {
       switch (_context2.prev = _context2.next) {
         case 0:
-          adapter = new _BamAdapter["default"](_configSchema["default"].create({
+          adapter = new _BamAdapter.default(_configSchema.default.create({
             bamLocation: {
               localPath: require.resolve('../../test_data/volvox-sorted.bam'),
               locationType: 'LocalPathLocation'
@@ -135,13 +135,13 @@ test('test usage of BamSlightlyLazyFeature toJSON (used in the widget)', /*#__PU
     }
   }, _callee2);
 })));
-test('test usage of BamSlightlyLazyFeature for extended CIGAR', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+test('test usage of BamSlightlyLazyFeature for extended CIGAR', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
   var adapter, features, featuresArray, f;
-  return _regenerator["default"].wrap(function _callee3$(_context3) {
+  return _regenerator.default.wrap(function _callee3$(_context3) {
     while (1) {
       switch (_context3.prev = _context3.next) {
         case 0:
-          adapter = new _BamAdapter["default"](_configSchema["default"].create({
+          adapter = new _BamAdapter.default(_configSchema.default.create({
             bamLocation: {
               localPath: require.resolve('../../test_data/extended_cigar.bam'),
               locationType: 'LocalPathLocation'

package/dist/BamAdapter/BamSlightlyLazyFeature.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 _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
@@ -19,19 +19,19 @@ var _MismatchParser = require("./MismatchParser");
 
 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 BamSlightlyLazyFeature = /*#__PURE__*/function () {
   // uses parameter properties to automatically create fields on the class
   // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
   function BamSlightlyLazyFeature(record, adapter, ref) {
-    (0, _classCallCheck2["default"])(this, BamSlightlyLazyFeature);
+    (0, _classCallCheck2.default)(this, BamSlightlyLazyFeature);
     this.record = record;
     this.adapter = adapter;
     this.ref = ref;
   }
 
-  (0, _createClass2["default"])(BamSlightlyLazyFeature, [{
+  (0, _createClass2.default)(BamSlightlyLazyFeature, [{
     key: "_get_name",
     value: function _get_name() {
       return this.record.get('name');
@@ -101,7 +101,7 @@ var BamSlightlyLazyFeature = /*#__PURE__*/function () {
     key: "tags",
     value: function tags() {
       var properties = Object.getOwnPropertyNames(BamSlightlyLazyFeature.prototype);
-      return (0, _toConsumableArray2["default"])(new Set(properties.filter(function (prop) {
+      return (0, _toConsumableArray2.default)(new Set(properties.filter(function (prop) {
         return prop.startsWith('_get_') && prop !== '_get_mismatches' && prop !== '_get_tags' && prop !== '_get_next_seq_id' && prop !== '_get_seq_id';
       }).map(function (methodName) {
         return methodName.replace('_get_', '');
@@ -173,4 +173,4 @@ var BamSlightlyLazyFeature = /*#__PURE__*/function () {
   return BamSlightlyLazyFeature;
 }();
 
-exports["default"] = BamSlightlyLazyFeature;
+exports.default = BamSlightlyLazyFeature;

package/dist/BamAdapter/MismatchParser.js

@@ -21,7 +21,7 @@ var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"))
 
 var _util = require("@jbrowse/core/util");
 
-var _marked = /*#__PURE__*/_regenerator["default"].mark(getNextRefPos);
+var _marked = /*#__PURE__*/_regenerator.default.mark(getNextRefPos);
 
 var mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
 
@@ -244,7 +244,7 @@ function getMismatches(cigar, md, seq, ref, qual) {
 
 function getNextRefPos(cigarOps, positions) {
   var cigarIdx, readPos, refPos, i, pos, len, op;
-  return _regenerator["default"].wrap(function getNextRefPos$(_context) {
+  return _regenerator.default.wrap(function getNextRefPos$(_context) {
     while (1) {
       switch (_context.prev = _context.next) {
         case 0:
@@ -297,7 +297,7 @@ function getModificationPositions(mm, fseq, fstrand) {
     return !!mod;
   }).map(function (mod) {
     var _mod$split = mod.split(','),
-        _mod$split2 = (0, _toArray2["default"])(_mod$split),
+        _mod$split2 = (0, _toArray2.default)(_mod$split),
         basemod = _mod$split2[0],
         skips = _mod$split2.slice(1); // regexes based on parse_mm.pl from hts-specs
 
@@ -308,7 +308,7 @@ function getModificationPositions(mm, fseq, fstrand) {
       throw new Error('bad format for MM tag');
     }
 
-    var _matches = (0, _slicedToArray2["default"])(matches, 4),
+    var _matches = (0, _slicedToArray2.default)(matches, 4),
         base = _matches[1],
         strand = _matches[2],
         typestr = _matches[3]; // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
@@ -363,7 +363,7 @@ function getModificationTypes(mm) {
     return !!mod;
   }).map(function (mod) {
     var _mod$split3 = mod.split(','),
-        _mod$split4 = (0, _slicedToArray2["default"])(_mod$split3, 1),
+        _mod$split4 = (0, _slicedToArray2.default)(_mod$split3, 1),
         basemod = _mod$split4[0];
 
     var matches = basemod.match(/([A-Z])([-+])([^,]+)/);
@@ -372,7 +372,7 @@ function getModificationTypes(mm) {
       throw new Error('bad format for MM tag');
     }
 
-    var _matches2 = (0, _slicedToArray2["default"])(matches, 4),
+    var _matches2 = (0, _slicedToArray2.default)(matches, 4),
         typestr = _matches2[3]; // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
     // split, and they can also be chemical codes (ChEBI) e.g. C+16061
 

package/dist/BamAdapter/MismatchParser.test.js

@@ -220,7 +220,7 @@ test('getNextRefPos basic', function () {
   var cigar = (0, _MismatchParser.parseCigar)('10S10M1I4M1D15M');
   var iter = (0, _MismatchParser.getNextRefPos)(cigar, [5, 10, 15, 20, 25, 30, 35]);
 
-  var _iter = (0, _toArray2["default"])(iter),
+  var _iter = (0, _toArray2.default)(iter),
       vals = _iter.slice(0);
 
   expect(vals).toEqual([-5, 0, 5, 10, 14, 20, 25]);
@@ -229,7 +229,7 @@ test('getNextRefPos with many indels', function () {
   var cigar = (0, _MismatchParser.parseCigar)('10S4M1D1IM10');
   var iter = (0, _MismatchParser.getNextRefPos)(cigar, [5, 10, 15]);
 
-  var _iter2 = (0, _toArray2["default"])(iter),
+  var _iter2 = (0, _toArray2.default)(iter),
       vals = _iter2.slice(0);
 
   expect(vals).toEqual([-5, 0, 5]);

package/dist/BamAdapter/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");
 
@@ -45,4 +45,4 @@ var _default = _mobxStateTree.types.late(function () {
   });
 });
 
-exports["default"] = _default;
+exports.default = _default;