@jbrowse/plugin-alignments 1.7.0 → 1.7.4

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -1,71 +1,67 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-interface SNPCoverageOptions extends BaseOptions {
-    filters?: SerializableFilterChain;
-}
-export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
-    protected configure(): Promise<{
-        subadapter: BaseFeatureDataAdapter;
-        sequenceAdapter: BaseFeatureDataAdapter | undefined;
-    }>;
-    fetchSequence(region: Region): Promise<any>;
-    getFeatures(region: Region, opts?: SNPCoverageOptions): import("rxjs").Observable<Feature>;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    freeResources(): void;
-    generateCoverageBins(features: Feature[], region: Region, opts: {
-        bpPerPx?: number;
-        colorBy?: {
-            type: string;
-            tag?: string;
-        };
-    }): Promise<{
-        bins: {
-            total: number;
-            lowqual: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            cov: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            delskips: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            noncov: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            ref: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-        }[];
-        skipmap: {
-            [key: string]: {
-                score: number;
-                feature: unknown;
-                start: number;
-                end: number;
-                strand: number;
-                xs: string;
-            };
-        };
-    }>;
-}
-declare const capabilities: string[];
-export { capabilities };
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
+    protected configure(): Promise<{
+        subadapter: BaseFeatureDataAdapter;
+        sequenceAdapter: BaseFeatureDataAdapter | undefined;
+    }>;
+    fetchSequence(region: Region): Promise<any>;
+    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    freeResources(): void;
+    generateCoverageBins(features: Feature[], region: Region, opts: {
+        bpPerPx?: number;
+        colorBy?: {
+            type: string;
+            tag?: string;
+        };
+    }): Promise<{
+        bins: {
+            total: number;
+            lowqual: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+            cov: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+            delskips: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+            noncov: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+            ref: {
+                total: number;
+                strands: {
+                    [key: string]: number;
+                };
+            };
+        }[];
+        skipmap: {
+            [key: string]: {
+                score: number;
+                feature: unknown;
+                start: number;
+                end: number;
+                strand: number;
+                xs: string;
+            };
+        };
+    }>;
+}
+declare const capabilities: string[];
+export { capabilities };

package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = exports.capabilities = void 0;
+exports.default = exports.capabilities = void 0;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -35,13 +35,13 @@ var _util = require("../util");
 
 var _MismatchParser = require("../BamAdapter/MismatchParser");
 
-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; } }
 
@@ -90,23 +90,23 @@ function dec(bin, strand, type, field) {
 }
 
 var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2["default"])(SNPCoverageAdapter, _BaseFeatureDataAdapt);
+  (0, _inherits2.default)(SNPCoverageAdapter, _BaseFeatureDataAdapt);
 
   var _super = _createSuper(SNPCoverageAdapter);
 
   function SNPCoverageAdapter() {
-    (0, _classCallCheck2["default"])(this, SNPCoverageAdapter);
+    (0, _classCallCheck2.default)(this, SNPCoverageAdapter);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2["default"])(SNPCoverageAdapter, [{
+  (0, _createClass2.default)(SNPCoverageAdapter, [{
     key: "configure",
     value: function () {
-      var _configure = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+      var _configure = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
         var _this$getSubAdapter, _this$getSubAdapter2;
 
         var subadapterConfig, sequenceConf, dataAdapter, sequenceAdapter;
-        return _regenerator["default"].wrap(function _callee$(_context) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -167,10 +167,10 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "fetchSequence",
     value: function () {
-      var _fetchSequence2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(region) {
+      var _fetchSequence2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(region) {
         var _yield$this$configure, sequenceAdapter;
 
-        return _regenerator["default"].wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -212,10 +212,10 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
       return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(observer) {
+        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(observer) {
           var _yield$_this$configur, subadapter, feats, _yield$_this$generate, bins, skipmap;
 
-          return _regenerator["default"].wrap(function _callee3$(_context3) {
+          return _regenerator.default.wrap(function _callee3$(_context3) {
             while (1) {
               switch (_context3.prev = _context3.next) {
                 case 0:
@@ -238,7 +238,7 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   bins = _yield$_this$generate.bins;
                   skipmap = _yield$_this$generate.skipmap;
                   bins.forEach(function (bin, index) {
-                    observer.next(new _simpleFeature["default"]({
+                    observer.next(new _simpleFeature.default({
                       id: "".concat(_this.id, "-").concat(region.start + index),
                       data: {
                         score: bin.total,
@@ -251,11 +251,11 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   }); // make fake features from the coverage
 
                   Object.entries(skipmap).forEach(function (_ref2) {
-                    var _ref3 = (0, _slicedToArray2["default"])(_ref2, 2),
+                    var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
                         key = _ref3[0],
                         skip = _ref3[1];
 
-                    observer.next(new _simpleFeature["default"]({
+                    observer.next(new _simpleFeature.default({
                       id: key,
                       data: {
                         type: 'skip',
@@ -285,10 +285,10 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "estimateRegionsStats",
     value: function () {
-      var _estimateRegionsStats = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(regions, opts) {
+      var _estimateRegionsStats = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(regions, opts) {
         var _yield$this$configure2, subadapter;
 
-        return _regenerator["default"].wrap(function _callee4$(_context4) {
+        return _regenerator.default.wrap(function _callee4$(_context4) {
           while (1) {
             switch (_context4.prev = _context4.next) {
               case 0:
@@ -317,13 +317,13 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getRefNames",
     value: function () {
-      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5() {
+      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
         var opts,
             _yield$this$configure3,
             subadapter,
             _args5 = arguments;
 
-        return _regenerator["default"].wrap(function _callee5$(_context5) {
+        return _regenerator.default.wrap(function _callee5$(_context5) {
           while (1) {
             switch (_context5.prev = _context5.next) {
               case 0:
@@ -358,12 +358,12 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "generateCoverageBins",
     value: function () {
-      var _generateCoverageBins = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee6(features, region, opts) {
+      var _generateCoverageBins = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(features, region, opts) {
         var _opts$colorBy;
 
         var colorBy, binMax, skipmap, regionSeq, bins, _loop, i;
 
-        return _regenerator["default"].wrap(function _callee6$(_context6) {
+        return _regenerator.default.wrap(function _callee6$(_context6) {
           while (1) {
             switch (_context6.prev = _context6.next) {
               case 0:
@@ -601,6 +601,6 @@ var SNPCoverageAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   return SNPCoverageAdapter;
 }(_BaseAdapter.BaseFeatureDataAdapter);
 
-exports["default"] = SNPCoverageAdapter;
+exports.default = SNPCoverageAdapter;
 var capabilities = SNPCoverageAdapter.capabilities;
 exports.capabilities = capabilities;

package/dist/SNPCoverageAdapter/configSchema.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/SNPCoverageAdapter/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");
 
@@ -19,4 +19,4 @@ var _default = function _default(pluginManager) {
   });
 };
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/SNPCoverageAdapter/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/dist/SNPCoverageAdapter/index.js

@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports["default"] = void 0;
+exports.default = void 0;
 
 var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
@@ -17,11 +17,11 @@ var _SNPCoverageAdapter = require("./SNPCoverageAdapter");
 
 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 _default = function _default(pluginManager) {
   pluginManager.addAdapterType(function () {
-    return new _AdapterType["default"]({
+    return new _AdapterType.default({
       name: 'SNPCoverageAdapter',
       adapterMetadata: {
         category: null,
@@ -33,13 +33,13 @@ var _default = function _default(pluginManager) {
         return Promise.resolve().then(function () {
           return _interopRequireWildcard(require('./SNPCoverageAdapter'));
         }).then(function (r) {
-          return r["default"];
+          return r.default;
         });
       },
-      configSchema: (0, _configSchema["default"])(pluginManager),
+      configSchema: (0, _configSchema.default)(pluginManager),
       adapterCapabilities: _SNPCoverageAdapter.capabilities
     });
   });
 };
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.d.ts

@@ -1,20 +1,20 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
-export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
-    bpPerPx: number;
-    height: number;
-    highResolutionScaling: number;
-    scaleOpts: ScaleOpts;
-}
-export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
-    features: Map<string, Feature>;
-    ticks: {
-        values: number[];
-    };
-    displayCrossHatches: boolean;
-    modificationTagMap?: Record<string, string>;
-}
-export default class SNPCoverageRenderer extends WiggleBaseRenderer {
-    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): void;
-}
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
+export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+    bpPerPx: number;
+    height: number;
+    highResolutionScaling: number;
+    scaleOpts: ScaleOpts;
+}
+export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+    ticks: {
+        values: number[];
+    };
+    displayCrossHatches: boolean;
+    modificationTagMap?: Record<string, string>;
+}
+export default class SNPCoverageRenderer extends WiggleBaseRenderer {
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): void;
+}

package/dist/SNPCoverageRenderer/SNPCoverageRenderer.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"));
 
@@ -33,23 +33,23 @@ var _pluginWiggle = require("@jbrowse/plugin-wiggle");
 
 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; } }
 
 var SNPCoverageRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
-  (0, _inherits2["default"])(SNPCoverageRenderer, _WiggleBaseRenderer);
+  (0, _inherits2.default)(SNPCoverageRenderer, _WiggleBaseRenderer);
 
   var _super = _createSuper(SNPCoverageRenderer);
 
   function SNPCoverageRenderer() {
-    (0, _classCallCheck2["default"])(this, SNPCoverageRenderer);
+    (0, _classCallCheck2.default)(this, SNPCoverageRenderer);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2["default"])(SNPCoverageRenderer, [{
+  (0, _createClass2.default)(SNPCoverageRenderer, [{
     key: "draw",
     value: // note: the snps are drawn on linear scale even if the data is drawn in log
     // scape hence the two different scales being used
@@ -67,7 +67,7 @@ var SNPCoverageRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
           ticks = props.ticks;
       var theme = (0, _ui.createJBrowseTheme)(configTheme);
 
-      var _regions = (0, _slicedToArray2["default"])(regions, 1),
+      var _regions = (0, _slicedToArray2.default)(regions, 1),
           region = _regions[0];
 
       var width = (region.end - region.start) / bpPerPx; // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the
@@ -127,7 +127,7 @@ var SNPCoverageRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
         unmeth: 'blue',
         ref: 'lightgrey'
       };
-      var feats = (0, _toConsumableArray2["default"])(features.values());
+      var feats = (0, _toConsumableArray2.default)(features.values());
       var coverage = feats.filter(function (f) {
         return f.get('type') !== 'skip';
       });
@@ -142,7 +142,7 @@ var SNPCoverageRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
         var feature = coverage[i];
 
         var _featureSpanPx = (0, _util.featureSpanPx)(feature, region, bpPerPx),
-            _featureSpanPx2 = (0, _slicedToArray2["default"])(_featureSpanPx, 2),
+            _featureSpanPx2 = (0, _slicedToArray2.default)(_featureSpanPx, 2),
             leftPx = _featureSpanPx2[0],
             rightPx = _featureSpanPx2[1];
 
@@ -167,7 +167,7 @@ var SNPCoverageRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
         var _feature = coverage[_i];
 
         var _featureSpanPx3 = (0, _util.featureSpanPx)(_feature, region, bpPerPx),
-            _featureSpanPx4 = (0, _slicedToArray2["default"])(_featureSpanPx3, 2),
+            _featureSpanPx4 = (0, _slicedToArray2.default)(_featureSpanPx3, 2),
             _leftPx = _featureSpanPx4[0],
             _rightPx = _featureSpanPx4[1];
 
@@ -248,7 +248,7 @@ var SNPCoverageRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
           var f = skips[_i5];
 
           var _bpSpanPx = (0, _util.bpSpanPx)(f.get('start'), f.get('end'), region, bpPerPx),
-              _bpSpanPx2 = (0, _slicedToArray2["default"])(_bpSpanPx, 2),
+              _bpSpanPx2 = (0, _slicedToArray2.default)(_bpSpanPx, 2),
               left = _bpSpanPx2[0],
               right = _bpSpanPx2[1];
 
@@ -293,4 +293,4 @@ var SNPCoverageRenderer = /*#__PURE__*/function (_WiggleBaseRenderer) {
   return SNPCoverageRenderer;
 }(_pluginWiggle.WiggleBaseRenderer);
 
-exports["default"] = SNPCoverageRenderer;
+exports.default = SNPCoverageRenderer;

package/dist/SNPCoverageRenderer/configSchema.d.ts

@@ -1,2 +1,2 @@
-declare var _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default _default;
+declare var _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/SNPCoverageRenderer/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");
 
@@ -37,4 +37,4 @@ var _default = (0, _configuration.ConfigurationSchema)('SNPCoverageRenderer', {
   explicitlyTyped: true
 });
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/SNPCoverageRenderer/index.d.ts

@@ -1,3 +1,3 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-export default function register(pluginManager: PluginManager): void;
+import PluginManager from '@jbrowse/core/PluginManager';
+export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default function register(pluginManager: PluginManager): void;

package/dist/SNPCoverageRenderer/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.configSchema = void 0;
-exports["default"] = register;
+exports.default = register;
 
 var _configuration = require("@jbrowse/core/configuration");
 
@@ -17,14 +17,14 @@ var _SNPCoverageRenderer = _interopRequireDefault(require("./SNPCoverageRenderer
 var _pluginWiggle = require("@jbrowse/plugin-wiggle");
 
 var configSchema = (0, _configuration.ConfigurationSchema)('SNPCoverageRenderer', {}, {
-  baseConfiguration: _configSchema["default"],
+  baseConfiguration: _configSchema.default,
   explicitlyTyped: true
 });
 exports.configSchema = configSchema;
 
 function register(pluginManager) {
   pluginManager.addRendererType(function () {
-    return new _SNPCoverageRenderer["default"]({
+    return new _SNPCoverageRenderer.default({
       name: 'SNPCoverageRenderer',
       ReactComponent: _pluginWiggle.WiggleRendering,
       configSchema: configSchema,

package/dist/index.d.ts

@@ -1,10 +1,10 @@
-import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-import * as MismatchParser from './BamAdapter/MismatchParser';
-import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
-export { MismatchParser };
-export type { LinearPileupDisplayModel };
-export default class AlignmentsPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+import * as MismatchParser from './BamAdapter/MismatchParser';
+import { LinearPileupDisplayModel } from './LinearPileupDisplay/model';
+export { MismatchParser };
+export type { LinearPileupDisplayModel };
+export default class AlignmentsPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}