@jbrowse/plugin-alignments 1.7.3 → 1.7.6

package/dist/NestedFrequencyTable.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 _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
 
@@ -15,7 +15,7 @@ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/de
 
 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; }
 
 /* eslint-disable @typescript-eslint/no-explicit-any */
 // see perf results on object.keys vs for-in loop
@@ -23,13 +23,13 @@ function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { va
 var NestedFrequencyTable = /*#__PURE__*/function () {
   function NestedFrequencyTable() {
     var initialData = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
-    (0, _classCallCheck2["default"])(this, NestedFrequencyTable);
-    (0, _defineProperty2["default"])(this, "categories", void 0);
+    (0, _classCallCheck2.default)(this, NestedFrequencyTable);
+    (0, _defineProperty2.default)(this, "categories", void 0);
     this.categories = _objectSpread({}, initialData);
   } // get the sum of all the category counts
 
 
-  (0, _createClass2["default"])(NestedFrequencyTable, [{
+  (0, _createClass2.default)(NestedFrequencyTable, [{
     key: "total",
     value: function total() {
       // calculate total if necessary
@@ -104,7 +104,7 @@ var NestedFrequencyTable = /*#__PURE__*/function () {
 
       if (!slot || !slot.categories) {
         this.categories[slotName] = new NestedFrequencyTable(slot ? {
-          "default": slot + 0
+          default: slot + 0
         } : {});
       }
 
@@ -149,4 +149,4 @@ var NestedFrequencyTable = /*#__PURE__*/function () {
   return NestedFrequencyTable;
 }();
 
-exports["default"] = NestedFrequencyTable;
+exports.default = NestedFrequencyTable;

package/dist/PileupRPC/rpcMethods.js

@@ -41,37 +41,37 @@ var _util2 = require("../util");
 
 var _MismatchParser = require("../BamAdapter/MismatchParser");
 
-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 PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
-  (0, _inherits2["default"])(PileupGetGlobalValueForTag, _RpcMethodType);
+  (0, _inherits2.default)(PileupGetGlobalValueForTag, _RpcMethodType);
 
   var _super = _createSuper(PileupGetGlobalValueForTag);
 
   function PileupGetGlobalValueForTag() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, PileupGetGlobalValueForTag);
+    (0, _classCallCheck2.default)(this, PileupGetGlobalValueForTag);
 
     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), "name", 'PileupGetGlobalValueForTag');
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'PileupGetGlobalValueForTag');
     return _this;
   }
 
-  (0, _createClass2["default"])(PileupGetGlobalValueForTag, [{
+  (0, _createClass2.default)(PileupGetGlobalValueForTag, [{
     key: "serializeArguments",
     value: function () {
-      var _serializeArguments = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(args, rpcDriverClassName) {
+      var _serializeArguments = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(args, rpcDriverClassName) {
         var _rootModel$session;
 
         var rootModel, assemblyManager, renamedArgs;
-        return _regenerator["default"].wrap(function _callee$(_context) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -91,7 +91,7 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
 
               case 6:
                 renamedArgs = _context.sent;
-                return _context.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupGetGlobalValueForTag.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
+                return _context.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(PileupGetGlobalValueForTag.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
 
               case 8:
               case "end":
@@ -110,9 +110,9 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
   }, {
     key: "execute",
     value: function () {
-      var _execute = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(args, rpcDriverClassName) {
+      var _execute = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(args, rpcDriverClassName) {
         var deserializedArgs, adapterConfig, sessionId, regions, tag, dataAdapter, features, featuresArray, uniqueValues;
-        return _regenerator["default"].wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -142,7 +142,7 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
                     uniqueValues.add("".concat(val));
                   }
                 });
-                return _context2.abrupt("return", (0, _toConsumableArray2["default"])(uniqueValues));
+                return _context2.abrupt("return", (0, _toConsumableArray2.default)(uniqueValues));
 
               case 14:
               case "end":
@@ -160,37 +160,37 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
     }()
   }]);
   return PileupGetGlobalValueForTag;
-}(_RpcMethodType3["default"]);
+}(_RpcMethodType3.default);
 
 exports.PileupGetGlobalValueForTag = PileupGetGlobalValueForTag;
 
 var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
-  (0, _inherits2["default"])(PileupGetVisibleModifications, _RpcMethodType2);
+  (0, _inherits2.default)(PileupGetVisibleModifications, _RpcMethodType2);
 
   var _super2 = _createSuper(PileupGetVisibleModifications);
 
   function PileupGetVisibleModifications() {
     var _this2;
 
-    (0, _classCallCheck2["default"])(this, PileupGetVisibleModifications);
+    (0, _classCallCheck2.default)(this, PileupGetVisibleModifications);
 
     for (var _len2 = arguments.length, args = new Array(_len2), _key2 = 0; _key2 < _len2; _key2++) {
       args[_key2] = arguments[_key2];
     }
 
     _this2 = _super2.call.apply(_super2, [this].concat(args));
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this2), "name", 'PileupGetVisibleModifications');
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this2), "name", 'PileupGetVisibleModifications');
     return _this2;
   }
 
-  (0, _createClass2["default"])(PileupGetVisibleModifications, [{
+  (0, _createClass2.default)(PileupGetVisibleModifications, [{
     key: "serializeArguments",
     value: function () {
-      var _serializeArguments2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(args, rpcDriverClassName) {
+      var _serializeArguments2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(args, rpcDriverClassName) {
         var _rootModel$session2;
 
         var rootModel, assemblyManager, renamedArgs;
-        return _regenerator["default"].wrap(function _callee3$(_context3) {
+        return _regenerator.default.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
@@ -210,7 +210,7 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
 
               case 6:
                 renamedArgs = _context3.sent;
-                return _context3.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupGetVisibleModifications.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
+                return _context3.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(PileupGetVisibleModifications.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
 
               case 8:
               case "end":
@@ -229,9 +229,9 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
   }, {
     key: "execute",
     value: function () {
-      var _execute2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(args, rpcDriverClassName) {
+      var _execute2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(args, rpcDriverClassName) {
         var deserializedArgs, adapterConfig, sessionId, regions, dataAdapter, features, featuresArray, uniqueValues;
-        return _regenerator["default"].wrap(function _callee4$(_context4) {
+        return _regenerator.default.wrap(function _callee4$(_context4) {
           while (1) {
             switch (_context4.prev = _context4.next) {
               case 0:
@@ -262,7 +262,7 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
                     });
                   }
                 });
-                return _context4.abrupt("return", (0, _toConsumableArray2["default"])(uniqueValues));
+                return _context4.abrupt("return", (0, _toConsumableArray2.default)(uniqueValues));
 
               case 14:
               case "end":
@@ -280,6 +280,6 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
     }()
   }]);
   return PileupGetVisibleModifications;
-}(_RpcMethodType3["default"]);
+}(_RpcMethodType3.default);
 
 exports.PileupGetVisibleModifications = PileupGetVisibleModifications;

package/dist/PileupRenderer/PileupLayoutSession.js

@@ -29,33 +29,33 @@ var _BoxRendererType = require("@jbrowse/core/pluggableElementTypes/renderers/Bo
 
 var _configuration = require("@jbrowse/core/configuration");
 
-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; } }
 
 // Sorting and revealing soft clip changes the layout of Pileup renderer
 // Adds extra conditions to see if cached layout is valid
 var PileupLayoutSession = /*#__PURE__*/function (_LayoutSession) {
-  (0, _inherits2["default"])(PileupLayoutSession, _LayoutSession);
+  (0, _inherits2.default)(PileupLayoutSession, _LayoutSession);
 
   var _super = _createSuper(PileupLayoutSession);
 
   function PileupLayoutSession(args) {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, PileupLayoutSession);
+    (0, _classCallCheck2.default)(this, PileupLayoutSession);
     _this = _super.call(this, args);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "sortedBy", void 0);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "showSoftClip", false);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "cachedLayout", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "sortedBy", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "showSoftClip", false);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "cachedLayout", void 0);
     _this.config = args.config;
     return _this;
   }
 
-  (0, _createClass2["default"])(PileupLayoutSession, [{
+  (0, _createClass2.default)(PileupLayoutSession, [{
     key: "cachedLayoutIsValid",
     value: function cachedLayoutIsValid(cachedLayout) {
-      return (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupLayoutSession.prototype), "cachedLayoutIsValid", this).call(this, cachedLayout) && this.showSoftClip === cachedLayout.showSoftClip && (0, _fastDeepEqual["default"])(this.sortedBy, cachedLayout.sortedBy);
+      return (0, _get2.default)((0, _getPrototypeOf2.default)(PileupLayoutSession.prototype), "cachedLayoutIsValid", this).call(this, cachedLayout) && this.showSoftClip === cachedLayout.showSoftClip && (0, _fastDeepEqual.default)(this.sortedBy, cachedLayout.sortedBy);
     }
   }, {
     key: "layout",

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import BoxRendererType, { RenderArgs, RenderArgsSerialized, RenderArgsDeserialized as BoxRenderArgsDeserialized, RenderResults, ResultsSerialized, ResultsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { Theme } from '@material-ui/core';
 import { Region, Feature } from '@jbrowse/core/util';
@@ -102,7 +101,7 @@ export default class PileupRenderer extends BoxRendererType {
     layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
     fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
     render(renderProps: RenderArgsDeserialized): Promise<{
-        features: Map<string, Feature>;
+        features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
         height: number;
         width: number;
@@ -111,7 +110,7 @@ export default class PileupRenderer extends BoxRendererType {
         imageData?: undefined;
         html?: string | undefined;
     } | {
-        features: Map<string, Feature>;
+        features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
         height: number;
         width: number;

package/dist/PileupRenderer/PileupRenderer.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"));
 
@@ -51,7 +51,7 @@ var _util2 = require("../util");
 
 var _PileupLayoutSession = require("./PileupLayoutSession");
 
-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); }
 
@@ -59,9 +59,9 @@ function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len
 
 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 _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; } }
 
@@ -78,7 +78,7 @@ function getColorBaseMap(theme) {
 
 function getContrastBaseMap(theme) {
   return Object.fromEntries(Object.entries(getColorBaseMap(theme)).map(function (_ref) {
-    var _ref2 = (0, _slicedToArray2["default"])(_ref, 2),
+    var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
         key = _ref2[0],
         value = _ref2[1];
 
@@ -110,25 +110,25 @@ function shouldDrawMismatches(type) {
 }
 
 var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
-  (0, _inherits2["default"])(PileupRenderer, _BoxRendererType);
+  (0, _inherits2.default)(PileupRenderer, _BoxRendererType);
 
   var _super = _createSuper(PileupRenderer);
 
   function PileupRenderer() {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, PileupRenderer);
+    (0, _classCallCheck2.default)(this, PileupRenderer);
 
     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), "supportsSVG", true);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "supportsSVG", true);
     return _this;
   }
 
-  (0, _createClass2["default"])(PileupRenderer, [{
+  (0, _createClass2.default)(PileupRenderer, [{
     key: "getCharWidthHeight",
     value: // get width and height of chars the height is an approximation: width
     // letter M is approximately the height
@@ -173,7 +173,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
       }
 
       var _bpSpanPx = (0, _util.bpSpanPx)(feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, region, bpPerPx),
-          _bpSpanPx2 = (0, _slicedToArray2["default"])(_bpSpanPx, 2),
+          _bpSpanPx2 = (0, _slicedToArray2.default)(_bpSpanPx, 2),
           leftPx = _bpSpanPx2[0],
           rightPx = _bpSpanPx2[1];
 
@@ -185,7 +185,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
         throw new Error("feature ".concat(feature.id(), " is not on the current region's reference sequence ").concat(region.refName));
       }
 
-      var topPx = layout.addRect(feature.id(), feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, heightPx);
+      var topPx = layout.addRect(feature.id(), feature.get('start') - expansionBefore, feature.get('end') + expansionAfter, heightPx, feature);
 
       if (topPx === null) {
         return null;
@@ -302,7 +302,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
             ctx.fillStyle = colorForBase[letter];
 
             var _bpSpanPx3 = (0, _util.bpSpanPx)(start + roffset + m, start + roffset + m + 1, region, bpPerPx),
-                _bpSpanPx4 = (0, _slicedToArray2["default"])(_bpSpanPx3, 1),
+                _bpSpanPx4 = (0, _slicedToArray2.default)(_bpSpanPx3, 1),
                 leftPx = _bpSpanPx4[0];
 
             ctx.fillRect(leftPx, topPx, widthPx + 0.5, heightPx);
@@ -350,7 +350,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
             ctx.fillStyle = "hsl(".concat(score === 255 ? 150 : score * 1.5, ",55%,50%)");
 
             var _bpSpanPx5 = (0, _util.bpSpanPx)(start + roffset + m, start + roffset + m + 1, region, bpPerPx),
-                _bpSpanPx6 = (0, _slicedToArray2["default"])(_bpSpanPx5, 1),
+                _bpSpanPx6 = (0, _slicedToArray2.default)(_bpSpanPx5, 1),
                 leftPx = _bpSpanPx6[0];
 
             ctx.fillRect(leftPx, topPx, width + 0.5, heightPx);
@@ -404,7 +404,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
             type = _modifications$i.type,
             positions = _modifications$i.positions;
         var col = modificationTagMap[type] || 'black';
-        var base = (0, _color["default"])(col);
+        var base = (0, _color.default)(col);
 
         var _iterator = _createForOfIteratorHelper((0, _MismatchParser.getNextRefPos)(cigarOps, positions)),
             _step;
@@ -415,7 +415,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
 
             if (readPos >= 0 && start + readPos < end) {
               var _bpSpanPx7 = (0, _util.bpSpanPx)(start + readPos, start + readPos + 1, region, bpPerPx),
-                  _bpSpanPx8 = (0, _slicedToArray2["default"])(_bpSpanPx7, 2),
+                  _bpSpanPx8 = (0, _slicedToArray2.default)(_bpSpanPx7, 2),
                   leftPx = _bpSpanPx8[0],
                   rightPx = _bpSpanPx8[1]; // give it a little boost of 0.1 to not make them fully
               // invisible to avoid confusion
@@ -501,7 +501,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
               var s = rstart + _i;
 
               var _bpSpanPx9 = (0, _util.bpSpanPx)(s, s + 2, region, bpPerPx),
-                  _bpSpanPx10 = (0, _slicedToArray2["default"])(_bpSpanPx9, 2),
+                  _bpSpanPx10 = (0, _slicedToArray2.default)(_bpSpanPx9, 2),
                   leftPx = _bpSpanPx10[0],
                   rightPx = _bpSpanPx10[1];
 
@@ -520,7 +520,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
               var _s = rstart + _i;
 
               var _bpSpanPx11 = (0, _util.bpSpanPx)(_s, _s + 1, region, bpPerPx),
-                  _bpSpanPx12 = (0, _slicedToArray2["default"])(_bpSpanPx11, 2),
+                  _bpSpanPx12 = (0, _slicedToArray2.default)(_bpSpanPx11, 2),
                   _leftPx = _bpSpanPx12[0],
                   _rightPx = _bpSpanPx12[1];
 
@@ -533,7 +533,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
               ctx.fillRect(_leftPx, topPx, _rightPx - _leftPx + 0.5, heightPx);
 
               var _bpSpanPx13 = (0, _util.bpSpanPx)(_s + 1, _s + 2, region, bpPerPx),
-                  _bpSpanPx14 = (0, _slicedToArray2["default"])(_bpSpanPx13, 2),
+                  _bpSpanPx14 = (0, _slicedToArray2.default)(_bpSpanPx13, 2),
                   leftPx2 = _bpSpanPx14[0],
                   rightPx2 = _bpSpanPx14[1];
 
@@ -558,11 +558,11 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
           topPx = feat.topPx,
           feature = feat.feature;
 
-      var _regions = (0, _slicedToArray2["default"])(regions, 1),
+      var _regions = (0, _slicedToArray2.default)(regions, 1),
           region = _regions[0];
 
       var _bpSpanPx15 = (0, _util.bpSpanPx)(feature.get('start'), feature.get('end'), region, bpPerPx),
-          _bpSpanPx16 = (0, _slicedToArray2["default"])(_bpSpanPx15, 2),
+          _bpSpanPx16 = (0, _slicedToArray2.default)(_bpSpanPx15, 2),
           leftPx = _bpSpanPx16[0],
           rightPx = _bpSpanPx16[1];
 
@@ -746,7 +746,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
           topPx = feat.topPx,
           feature = feat.feature;
 
-      var _regions2 = (0, _slicedToArray2["default"])(regions, 1),
+      var _regions2 = (0, _slicedToArray2.default)(regions, 1),
           region = _regions2[0];
 
       var start = feature.get('start');
@@ -759,7 +759,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
         var color = baseColor;
 
         if (mismatchAlpha && mismatch.qual !== undefined) {
-          color = (0, _color["default"])(baseColor).alpha(Math.min(1, mismatch.qual / 50)).hsl().string();
+          color = (0, _color.default)(baseColor).alpha(Math.min(1, mismatch.qual / 50)).hsl().string();
         }
 
         return color;
@@ -777,7 +777,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
         var mbase = mismatch.base;
 
         var _bpSpanPx17 = (0, _util.bpSpanPx)(mstart, mstart + mlen, region, bpPerPx),
-            _bpSpanPx18 = (0, _slicedToArray2["default"])(_bpSpanPx17, 2),
+            _bpSpanPx18 = (0, _slicedToArray2.default)(_bpSpanPx17, 2),
             leftPx = _bpSpanPx18[0],
             rightPx = _bpSpanPx18[1];
 
@@ -809,7 +809,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
           ctx.fillStyle = 'purple';
           var pos = leftPx + extraHorizontallyFlippedOffset;
           var len = +mismatch.base || mismatch.length;
-          var insW = Math.max(minSubfeatureWidth, Math.min(1.2, 1 / bpPerPx));
+          var insW = Math.max(minSubfeatureWidth / 2, Math.min(1.2, 1 / bpPerPx));
 
           if (len < 10) {
             ctx.fillRect(pos, topPx, insW, heightPx);
@@ -856,7 +856,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
           var _mlen = _mismatch.length;
 
           var _bpSpanPx19 = (0, _util.bpSpanPx)(_mstart, _mstart + _mlen, region, bpPerPx),
-              _bpSpanPx20 = (0, _slicedToArray2["default"])(_bpSpanPx19, 1),
+              _bpSpanPx20 = (0, _slicedToArray2.default)(_bpSpanPx19, 1),
               _leftPx2 = _bpSpanPx20[0];
 
           var _len2 = +_mismatch.base || _mismatch.length;
@@ -892,7 +892,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
       var regions = props.regions,
           bpPerPx = props.bpPerPx;
 
-      var _regions3 = (0, _slicedToArray2["default"])(regions, 1),
+      var _regions3 = (0, _slicedToArray2.default)(regions, 1),
           region = _regions3[0];
 
       var minFeatWidth = (0, _configuration.readConfObject)(config, 'minSubfeatureWidth');
@@ -929,7 +929,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
             }
 
             var _bpSpanPx21 = (0, _util.bpSpanPx)(softClipStart + k, softClipStart + k + 1, region, bpPerPx),
-                _bpSpanPx22 = (0, _slicedToArray2["default"])(_bpSpanPx21, 2),
+                _bpSpanPx22 = (0, _slicedToArray2.default)(_bpSpanPx21, 2),
                 softClipLeftPx = _bpSpanPx22[0],
                 softClipRightPx = _bpSpanPx22[1];
 
@@ -951,12 +951,12 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
   }, {
     key: "makeImageData",
     value: function () {
-      var _makeImageData = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(ctx, layoutRecords, props) {
+      var _makeImageData = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(ctx, layoutRecords, props) {
         var _this2 = this;
 
         var layout, config, showSoftClip, colorBy, configTheme, mismatchAlpha, minSubfeatureWidth, insertScale, defaultColor, theme, colorForBase, contrastForBase, _this$getCharWidthHei2, charWidth, charHeight;
 
-        return _regenerator["default"].wrap(function _callee$(_context) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -1046,7 +1046,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
           showSoftClip = props.showSoftClip,
           regions = props.regions;
 
-      var _regions4 = (0, _slicedToArray2["default"])(regions, 1),
+      var _regions4 = (0, _slicedToArray2.default)(regions, 1),
           region = _regions4[0];
 
       if (!layout) {
@@ -1076,10 +1076,10 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
   }, {
     key: "fetchSequence",
     value: function () {
-      var _fetchSequence2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(renderProps) {
+      var _fetchSequence2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(renderProps) {
         var sessionId, regions, adapterConfig, sequenceAdapter, _yield$getAdapter, dataAdapter, _regions5, region;
 
-        return _regenerator["default"].wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -1100,7 +1100,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
               case 6:
                 _yield$getAdapter = _context2.sent;
                 dataAdapter = _yield$getAdapter.dataAdapter;
-                _regions5 = (0, _slicedToArray2["default"])(regions, 1), region = _regions5[0];
+                _regions5 = (0, _slicedToArray2.default)(regions, 1), region = _regions5[0];
                 return _context2.abrupt("return", (0, _util2.fetchSequence)(region, dataAdapter));
 
               case 10:
@@ -1120,13 +1120,13 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
   }, {
     key: "render",
     value: function () {
-      var _render = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(renderProps) {
+      var _render = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(renderProps) {
         var _renderProps$colorBy,
             _this4 = this;
 
         var features, layout, regions, bpPerPx, layoutRecords, _regions6, region, regionSequence, end, start, width, height, res, results;
 
-        return _regenerator["default"].wrap(function _callee3$(_context3) {
+        return _regenerator.default.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
@@ -1141,7 +1141,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
                   features: features,
                   layout: layout
                 }));
-                _regions6 = (0, _slicedToArray2["default"])(regions, 1), region = _regions6[0]; // only need reference sequence if there are features and only for some
+                _regions6 = (0, _slicedToArray2.default)(regions, 1), region = _regions6[0]; // only need reference sequence if there are features and only for some
                 // cases
 
                 if (!(features.size && (0, _util2.shouldFetchReferenceSequence)((_renderProps$colorBy = renderProps.colorBy) === null || _renderProps$colorBy === void 0 ? void 0 : _renderProps$colorBy.type))) {
@@ -1177,7 +1177,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
               case 20:
                 res = _context3.sent;
                 _context3.next = 23;
-                return (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupRenderer.prototype), "render", this).call(this, _objectSpread(_objectSpread(_objectSpread({}, renderProps), res), {}, {
+                return (0, _get2.default)((0, _getPrototypeOf2.default)(PileupRenderer.prototype), "render", this).call(this, _objectSpread(_objectSpread(_objectSpread({}, renderProps), res), {}, {
                   features: features,
                   layout: layout,
                   height: height,
@@ -1187,7 +1187,7 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
               case 23:
                 results = _context3.sent;
                 return _context3.abrupt("return", _objectSpread(_objectSpread(_objectSpread({}, results), res), {}, {
-                  features: features,
+                  features: new Map(),
                   layout: layout,
                   height: height,
                   width: width,
@@ -1215,6 +1215,6 @@ var PileupRenderer = /*#__PURE__*/function (_BoxRendererType) {
     }
   }]);
   return PileupRenderer;
-}(_BoxRendererType2["default"]);
+}(_BoxRendererType2.default);
 
-exports["default"] = PileupRenderer;
+exports.default = PileupRenderer;