@jbrowse/plugin-alignments 1.7.0 → 1.7.4

package/dist/CramAdapter/CramAdapter.test.js

@@ -18,12 +18,12 @@ var _CramTestAdapters = require("./CramTestAdapters");
 
 var _configSchema = _interopRequireDefault(require("./configSchema"));
 
-var pluginManager = new _PluginManager["default"]();
-var configSchema = pluginManager.load(_configSchema["default"]);
+var pluginManager = new _PluginManager.default();
+var configSchema = pluginManager.load(_configSchema.default);
 
 var getVolvoxSequenceSubAdapter = /*#__PURE__*/function () {
-  var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
-    return _regenerator["default"].wrap(function _callee$(_context) {
+  var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
+    return _regenerator.default.wrap(function _callee$(_context) {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:
@@ -45,13 +45,13 @@ var getVolvoxSequenceSubAdapter = /*#__PURE__*/function () {
   };
 }();
 
-test('adapter can fetch features from volvox-sorted.cram', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+test('adapter can fetch features from volvox-sorted.cram', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
   var adapter, features, featuresArray, featuresJsonArray;
-  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 _CramAdapter["default"](configSchema.create({
+          adapter = new _CramAdapter.default(configSchema.create({
             cramLocation: {
               localPath: require.resolve('../../test_data/volvox-sorted.cram'),
               locationType: 'LocalPathLocation'
@@ -95,13 +95,13 @@ test('adapter can fetch features from volvox-sorted.cram', /*#__PURE__*/(0, _asy
     }
   }, _callee2);
 })));
-test('test usage of cramSlightlyLazyFeature toJSON (used in the widget)', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+test('test usage of cramSlightlyLazyFeature toJSON (used in the widget)', /*#__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 _CramAdapter["default"](configSchema.create({
+          adapter = new _CramAdapter.default(configSchema.create({
             cramLocation: {
               localPath: require.resolve('../../test_data/volvox-sorted.cram'),
               locationType: 'LocalPathLocation'

package/dist/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -1,49 +1,49 @@
-import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
-import CramAdapter from './CramAdapter';
-export interface Mismatch {
-    qual?: number;
-    start: number;
-    length: number;
-    type: string;
-    base: string;
-    altbase?: string;
-    seq?: string;
-    cliplen?: number;
-}
-export default class CramSlightlyLazyFeature implements Feature {
-    private record;
-    private _store;
-    constructor(record: any, _store: CramAdapter);
-    _get_name(): any;
-    _get_start(): number;
-    _get_end(): number;
-    _get_cram_read_features(): any;
-    _get_type(): string;
-    _get_score(): any;
-    _get_flags(): any;
-    _get_strand(): 1 | -1;
-    _read_group_id(): number | undefined;
-    _get_qual(): any;
-    qualRaw(): any;
-    _get_seq_id(): string | undefined;
-    _get_refName(): string | undefined;
-    _get_is_paired(): boolean;
-    _get_pair_orientation(): any;
-    _get_template_length(): any;
-    _get_next_seq_id(): string | undefined;
-    _get_next_pos(): any;
-    _get_next_segment_position(): string | undefined;
-    _get_tags(): any;
-    _get_seq(): any;
-    _get_CIGAR(): string;
-    tags(): string[];
-    id(): string;
-    get(field: string): any;
-    parent(): undefined | Feature;
-    children(): undefined | Feature[];
-    set(): void;
-    pairedFeature(): boolean;
-    _get_clipPos(): any;
-    toJSON(): SimpleFeatureSerialized;
-    _get_mismatches(): Mismatch[];
-}
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import CramAdapter from './CramAdapter';
+export interface Mismatch {
+    qual?: number;
+    start: number;
+    length: number;
+    type: string;
+    base: string;
+    altbase?: string;
+    seq?: string;
+    cliplen?: number;
+}
+export default class CramSlightlyLazyFeature implements Feature {
+    private record;
+    private _store;
+    constructor(record: any, _store: CramAdapter);
+    _get_name(): any;
+    _get_start(): number;
+    _get_end(): number;
+    _get_cram_read_features(): any;
+    _get_type(): string;
+    _get_score(): any;
+    _get_flags(): any;
+    _get_strand(): 1 | -1;
+    _read_group_id(): number | undefined;
+    _get_qual(): any;
+    qualRaw(): any;
+    _get_seq_id(): string | undefined;
+    _get_refName(): string | undefined;
+    _get_is_paired(): boolean;
+    _get_pair_orientation(): any;
+    _get_template_length(): any;
+    _get_next_seq_id(): string | undefined;
+    _get_next_pos(): any;
+    _get_next_segment_position(): string | undefined;
+    _get_tags(): any;
+    _get_seq(): any;
+    _get_CIGAR(): string;
+    tags(): string[];
+    id(): string;
+    get(field: string): any;
+    parent(): undefined | Feature;
+    children(): undefined | Feature[];
+    set(): void;
+    pairedFeature(): boolean;
+    _get_clipPos(): any;
+    toJSON(): SimpleFeatureSerialized;
+    _get_mismatches(): Mismatch[];
+}

package/dist/CramAdapter/CramSlightlyLazyFeature.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"));
 
@@ -17,7 +17,7 @@ var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/creat
 
 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 no-underscore-dangle */
 var CramSlightlyLazyFeature = /*#__PURE__*/function () {
@@ -25,12 +25,12 @@ var CramSlightlyLazyFeature = /*#__PURE__*/function () {
   // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
   function CramSlightlyLazyFeature(record, _store) {
-    (0, _classCallCheck2["default"])(this, CramSlightlyLazyFeature);
+    (0, _classCallCheck2.default)(this, CramSlightlyLazyFeature);
     this.record = record;
     this._store = _store;
   }
 
-  (0, _createClass2["default"])(CramSlightlyLazyFeature, [{
+  (0, _createClass2.default)(CramSlightlyLazyFeature, [{
     key: "_get_name",
     value: function _get_name() {
       return this.record.readName;
@@ -180,7 +180,7 @@ var CramSlightlyLazyFeature = /*#__PURE__*/function () {
           if (code === 'b') {
             // An array of bases stored verbatim
             var ret = data.split(',');
-            var added = String.fromCharCode.apply(String, (0, _toConsumableArray2["default"])(ret));
+            var added = String.fromCharCode.apply(String, (0, _toConsumableArray2.default)(ret));
             seq += added;
             last_pos += added.length;
             oplen += added.length;
@@ -444,4 +444,4 @@ var CramSlightlyLazyFeature = /*#__PURE__*/function () {
   return CramSlightlyLazyFeature;
 }();
 
-exports["default"] = CramSlightlyLazyFeature;
+exports.default = CramSlightlyLazyFeature;

package/dist/CramAdapter/CramTestAdapters.d.ts

@@ -1,29 +1,29 @@
-import { GenericFilehandle } from 'generic-filehandle';
-import { Observable } from 'rxjs';
-import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-export declare function parseSmallFasta(text: string): {
-    id: string;
-    description: string;
-    sequence: string;
-}[];
-declare type FileHandle = GenericFilehandle;
-export declare class FetchableSmallFasta {
-    data: Promise<ReturnType<typeof parseSmallFasta>>;
-    constructor(filehandle: FileHandle);
-    fetch(id: number, start: number, end: number): Promise<string>;
-    getSequenceList(): Promise<string[]>;
-}
-export declare class SequenceAdapter extends BaseFeatureDataAdapter {
-    fasta: FetchableSmallFasta;
-    refNames: string[];
-    constructor(filehandle: FileHandle);
-    getRefNames(): Promise<string[]>;
-    getFeatures({ refName, start, end, }: {
-        refName: string;
-        start: number;
-        end: number;
-    }): Observable<SimpleFeature>;
-    freeResources(): void;
-}
-export {};
+import { GenericFilehandle } from 'generic-filehandle';
+import { Observable } from 'rxjs';
+import SimpleFeature from '@jbrowse/core/util/simpleFeature';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+export declare function parseSmallFasta(text: string): {
+    id: string;
+    description: string;
+    sequence: string;
+}[];
+declare type FileHandle = GenericFilehandle;
+export declare class FetchableSmallFasta {
+    data: Promise<ReturnType<typeof parseSmallFasta>>;
+    constructor(filehandle: FileHandle);
+    fetch(id: number, start: number, end: number): Promise<string>;
+    getSequenceList(): Promise<string[]>;
+}
+export declare class SequenceAdapter extends BaseFeatureDataAdapter {
+    fasta: FetchableSmallFasta;
+    refNames: string[];
+    constructor(filehandle: FileHandle);
+    getRefNames(): Promise<string[]>;
+    getFeatures({ refName, start, end, }: {
+        refName: string;
+        start: number;
+        end: number;
+    }): Observable<SimpleFeature>;
+    freeResources(): void;
+}
+export {};

package/dist/CramAdapter/CramTestAdapters.js

@@ -36,7 +36,7 @@ var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
 
 var _configurationSchema = require("@jbrowse/core/configuration/configurationSchema");
 
-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; } }
 
@@ -46,12 +46,12 @@ function parseSmallFasta(text) {
     return /\S/.test(t);
   }).map(function (entryText) {
     var _entryText$split = entryText.split('\n'),
-        _entryText$split2 = (0, _toArray2["default"])(_entryText$split),
+        _entryText$split2 = (0, _toArray2.default)(_entryText$split),
         defLine = _entryText$split2[0],
         seqLines = _entryText$split2.slice(1);
 
     var _defLine$split = defLine.split(' '),
-        _defLine$split2 = (0, _toArray2["default"])(_defLine$split),
+        _defLine$split2 = (0, _toArray2.default)(_defLine$split),
         id = _defLine$split2[0],
         descriptionLines = _defLine$split2.slice(1);
 
@@ -67,20 +67,20 @@ function parseSmallFasta(text) {
 
 var FetchableSmallFasta = /*#__PURE__*/function () {
   function FetchableSmallFasta(filehandle) {
-    (0, _classCallCheck2["default"])(this, FetchableSmallFasta);
-    (0, _defineProperty2["default"])(this, "data", void 0);
+    (0, _classCallCheck2.default)(this, FetchableSmallFasta);
+    (0, _defineProperty2.default)(this, "data", void 0);
     this.data = filehandle.readFile().then(function (buffer) {
       var text = buffer.toString('utf8');
       return parseSmallFasta(text);
     });
   }
 
-  (0, _createClass2["default"])(FetchableSmallFasta, [{
+  (0, _createClass2.default)(FetchableSmallFasta, [{
     key: "fetch",
     value: function () {
-      var _fetch = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(id, start, end) {
+      var _fetch = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(id, start, end) {
         var data, entry, length;
-        return _regenerator["default"].wrap(function _callee$(_context) {
+        return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
@@ -119,9 +119,9 @@ var FetchableSmallFasta = /*#__PURE__*/function () {
   }, {
     key: "getSequenceList",
     value: function () {
-      var _getSequenceList = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+      var _getSequenceList = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
         var data;
-        return _regenerator["default"].wrap(function _callee2$(_context2) {
+        return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
@@ -155,26 +155,26 @@ var FetchableSmallFasta = /*#__PURE__*/function () {
 exports.FetchableSmallFasta = FetchableSmallFasta;
 
 var SequenceAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2["default"])(SequenceAdapter, _BaseFeatureDataAdapt);
+  (0, _inherits2.default)(SequenceAdapter, _BaseFeatureDataAdapt);
 
   var _super = _createSuper(SequenceAdapter);
 
   function SequenceAdapter(filehandle) {
     var _this;
 
-    (0, _classCallCheck2["default"])(this, SequenceAdapter);
+    (0, _classCallCheck2.default)(this, SequenceAdapter);
     _this = _super.call(this, (0, _configurationSchema.ConfigurationSchema)('empty', {}).create());
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "fasta", void 0);
-    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "refNames", []);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "fasta", void 0);
+    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "refNames", []);
     _this.fasta = new FetchableSmallFasta(filehandle);
     return _this;
   }
 
-  (0, _createClass2["default"])(SequenceAdapter, [{
+  (0, _createClass2.default)(SequenceAdapter, [{
     key: "getRefNames",
     value: function () {
-      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
-        return _regenerator["default"].wrap(function _callee3$(_context3) {
+      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+        return _regenerator.default.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
@@ -208,7 +208,7 @@ var SequenceAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
         }).then(function () {
           return _this2.fasta.fetch(_this2.refNames.indexOf(refName), start, end);
         }).then(function (ret) {
-          observer.next(new _simpleFeature["default"]({
+          observer.next(new _simpleFeature.default({
             uniqueId: "".concat(refName, "-").concat(start, "-").concat(end),
             seq: ret,
             start: start,

package/dist/CramAdapter/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/CramAdapter/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 = function _default(pluginManager) {
   });
 };
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/CramAdapter/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/CramAdapter/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"));
 
@@ -15,22 +15,22 @@ var _configSchema = _interopRequireDefault(require("./configSchema"));
 
 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: 'CramAdapter',
-      configSchema: pluginManager.load(_configSchema["default"]),
+      configSchema: pluginManager.load(_configSchema.default),
       getAdapterClass: function getAdapterClass() {
         return Promise.resolve().then(function () {
           return _interopRequireWildcard(require('./CramAdapter'));
         }).then(function (r) {
-          return r["default"];
+          return r.default;
         });
       }
     });
   });
 };
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.d.ts

@@ -1,9 +1,9 @@
-import { BamFile } from '@gmod/bam';
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import BamAdapter from '../BamAdapter/BamAdapter';
-export default class HtsgetBamAdapter extends BamAdapter {
-    protected configure(): Promise<{
-        bam: BamFile;
-        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
-    }>;
-}
+import { BamFile } from '@gmod/bam';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import BamAdapter from '../BamAdapter/BamAdapter';
+export default class HtsgetBamAdapter extends BamAdapter {
+    protected configure(): Promise<{
+        bam: BamFile;
+        sequenceAdapter?: BaseFeatureDataAdapter | undefined;
+    }>;
+}

package/dist/HtsgetBamAdapter/HtsgetBamAdapter.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"));
 
@@ -27,26 +27,26 @@ var _configuration = require("@jbrowse/core/configuration");
 
 var _BamAdapter2 = _interopRequireDefault(require("../BamAdapter/BamAdapter"));
 
-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 HtsgetBamAdapter = /*#__PURE__*/function (_BamAdapter) {
-  (0, _inherits2["default"])(HtsgetBamAdapter, _BamAdapter);
+  (0, _inherits2.default)(HtsgetBamAdapter, _BamAdapter);
 
   var _super = _createSuper(HtsgetBamAdapter);
 
   function HtsgetBamAdapter() {
-    (0, _classCallCheck2["default"])(this, HtsgetBamAdapter);
+    (0, _classCallCheck2.default)(this, HtsgetBamAdapter);
     return _super.apply(this, arguments);
   }
 
-  (0, _createClass2["default"])(HtsgetBamAdapter, [{
+  (0, _createClass2.default)(HtsgetBamAdapter, [{
     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 htsgetBase, htsgetTrackId, 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:
@@ -92,6 +92,6 @@ var HtsgetBamAdapter = /*#__PURE__*/function (_BamAdapter) {
     }()
   }]);
   return HtsgetBamAdapter;
-}(_BamAdapter2["default"]);
+}(_BamAdapter2.default);
 
-exports["default"] = HtsgetBamAdapter;
+exports.default = HtsgetBamAdapter;

package/dist/HtsgetBamAdapter/configSchema.d.ts

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

package/dist/HtsgetBamAdapter/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");
 
@@ -28,4 +28,4 @@ var _default = _mobxStateTree.types.late(function () {
   });
 });
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/HtsgetBamAdapter/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/HtsgetBamAdapter/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"));
 
@@ -15,11 +15,11 @@ var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElemen
 
 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: 'HtsgetBamAdapter',
       adapterMetadata: {
         category: null,
@@ -27,16 +27,16 @@ var _default = function _default(pluginManager) {
         displayName: null,
         description: null
       },
-      configSchema: _configSchema["default"],
+      configSchema: _configSchema.default,
       getAdapterClass: function getAdapterClass() {
         return Promise.resolve().then(function () {
           return _interopRequireWildcard(require('./HtsgetBamAdapter'));
         }).then(function (r) {
-          return r["default"];
+          return r.default;
         });
       }
     });
   });
 };
 
-exports["default"] = _default;
+exports.default = _default;

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -1,7 +1,7 @@
-/// <reference types="react" />
-import { AlignmentsDisplayModel } from '../models/model';
-declare function AlignmentsDisplay({ model }: {
-    model: AlignmentsDisplayModel;
-}): JSX.Element;
-declare const _default: typeof AlignmentsDisplay;
-export default _default;
+/// <reference types="react" />
+import { AlignmentsDisplayModel } from '../models/model';
+declare function AlignmentsDisplay({ model }: {
+    model: AlignmentsDisplayModel;
+}): JSX.Element;
+declare const _default: typeof AlignmentsDisplay;
+export default _default;