@jbrowse/plugin-bed 1.7.2 → 1.7.5

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Files changed (12) hide show
  1. package/dist/BedTabixAdapter/BedTabixAdapter.js +22 -22
  2. package/dist/BedTabixAdapter/BedTabixAdapter.test.js +15 -15
  3. package/dist/BedTabixAdapter/configSchema.js +2 -2
  4. package/dist/BedTabixAdapter/index.js +1 -1
  5. package/dist/BigBedAdapter/BigBedAdapter.js +23 -23
  6. package/dist/BigBedAdapter/BigBedAdapter.test.js +3 -3
  7. package/dist/BigBedAdapter/configSchema.js +2 -2
  8. package/dist/BigBedAdapter/index.js +1 -1
  9. package/dist/index.js +13 -13
  10. package/dist/index.test.js +2 -2
  11. package/dist/util.js +1 -1
  12. package/package.json +4 -3
package/dist/BedTabixAdapter/BedTabixAdapter.js CHANGED
@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
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5
  Object.defineProperty(exports, "__esModule", {
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  value: true
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  });
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- exports["default"] = void 0;
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+ exports.default = void 0;
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  var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
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@@ -43,26 +43,26 @@ var _util = require("../util");
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  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; }
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- 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; }
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+ 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; }
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- 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); }; }
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+ 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); }; }
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  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; } }
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52
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  var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
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- (0, _inherits2["default"])(BedTabixAdapter, _BaseFeatureDataAdapt);
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+ (0, _inherits2.default)(BedTabixAdapter, _BaseFeatureDataAdapt);
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  var _super = _createSuper(BedTabixAdapter);
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  function BedTabixAdapter(config, getSubAdapter, pluginManager) {
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  var _this;
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- (0, _classCallCheck2["default"])(this, BedTabixAdapter);
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+ (0, _classCallCheck2.default)(this, BedTabixAdapter);
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  _this = _super.call(this, config, getSubAdapter, pluginManager);
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- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "parser", void 0);
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- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "bed", void 0);
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- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "columnNames", void 0);
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- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "scoreColumn", void 0);
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+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "parser", void 0);
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+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "bed", void 0);
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+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "columnNames", void 0);
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+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "scoreColumn", void 0);
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  var bedGzLocation = (0, _configuration.readConfObject)(config, 'bedGzLocation');
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  var index = (0, _configuration.readConfObject)(config, 'index');
68
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  var autoSql = (0, _configuration.readConfObject)(config, 'autoSql');
@@ -76,19 +76,19 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
76
76
  });
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  _this.columnNames = (0, _configuration.readConfObject)(config, 'columnNames');
78
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  _this.scoreColumn = (0, _configuration.readConfObject)(config, 'scoreColumn');
79
- _this.parser = new _bed["default"]({
79
+ _this.parser = new _bed.default({
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  autoSql: autoSql
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  });
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  return _this;
83
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  }
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85
- (0, _createClass2["default"])(BedTabixAdapter, [{
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+ (0, _createClass2.default)(BedTabixAdapter, [{
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  key: "getRefNames",
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  value: function () {
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- var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
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+ var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
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  var opts,
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  _args = arguments;
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- return _regenerator["default"].wrap(function _callee$(_context) {
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+ return _regenerator.default.wrap(function _callee$(_context) {
92
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  while (1) {
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  switch (_context.prev = _context.next) {
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  case 0:
@@ -112,8 +112,8 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
112
112
  }, {
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  key: "getHeader",
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  value: function () {
115
- var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
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- return _regenerator["default"].wrap(function _callee2$(_context2) {
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+ var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
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+ return _regenerator.default.wrap(function _callee2$(_context2) {
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  while (1) {
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  switch (_context2.prev = _context2.next) {
119
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  case 0:
@@ -143,9 +143,9 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
143
143
  }, {
144
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  key: "getNames",
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  value: function () {
146
- var _getNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
146
+ var _getNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
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  var header, defs, defline;
148
- return _regenerator["default"].wrap(function _callee3$(_context3) {
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+ return _regenerator.default.wrap(function _callee3$(_context3) {
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  while (1) {
150
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  switch (_context3.prev = _context3.next) {
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  case 0:
@@ -191,9 +191,9 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
191
191
 
192
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  var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
193
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  return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
194
- var _ref = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(observer) {
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+ var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(observer) {
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  var meta, columnNumbers, colRef, colStart, colEnd, colSame, names;
196
- return _regenerator["default"].wrap(function _callee4$(_context4) {
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+ return _regenerator.default.wrap(function _callee4$(_context4) {
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  while (1) {
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  switch (_context4.prev = _context4.next) {
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  case 0:
@@ -256,7 +256,7 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
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  delete data.chrom;
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  delete data.chromStart;
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  delete data.chromEnd;
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- var f = new _simpleFeature["default"](_objectSpread(_objectSpread({}, data), {}, {
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+ var f = new _simpleFeature.default(_objectSpread(_objectSpread({}, data), {}, {
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  start: start,
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  end: end,
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  refName: refName,
@@ -291,5 +291,5 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
291
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  return BedTabixAdapter;
292
292
  }(_BaseAdapter.BaseFeatureDataAdapter);
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293
 
294
- exports["default"] = BedTabixAdapter;
295
- (0, _defineProperty2["default"])(BedTabixAdapter, "capabilities", ['getFeatures', 'getRefNames']);
294
+ exports.default = BedTabixAdapter;
295
+ (0, _defineProperty2.default)(BedTabixAdapter, "capabilities", ['getFeatures', 'getRefNames']);
package/dist/BedTabixAdapter/BedTabixAdapter.test.js CHANGED
@@ -12,13 +12,13 @@ var _BedTabixAdapter = _interopRequireDefault(require("./BedTabixAdapter"));
12
12
 
13
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  var _configSchema = _interopRequireDefault(require("./configSchema"));
14
14
 
15
- test('adapter can fetch features from volvox-bed12.bed.gz', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
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+ test('adapter can fetch features from volvox-bed12.bed.gz', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
16
16
  var adapter, features, featuresArray, featuresJsonArray;
17
- return _regenerator["default"].wrap(function _callee$(_context) {
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+ return _regenerator.default.wrap(function _callee$(_context) {
18
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  while (1) {
19
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  switch (_context.prev = _context.next) {
20
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  case 0:
21
- adapter = new _BedTabixAdapter["default"](_configSchema["default"].create({
21
+ adapter = new _BedTabixAdapter.default(_configSchema.default.create({
22
22
  bedGzLocation: {
23
23
  localPath: require.resolve('./test_data/volvox-bed12.bed.gz'),
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  locationType: 'LocalPathLocation'
@@ -67,13 +67,13 @@ test('adapter can fetch features from volvox-bed12.bed.gz', /*#__PURE__*/(0, _as
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  }
68
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  }, _callee);
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  })));
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- test('adapter can fetch features from volvox.sort.bed.gz simple bed3', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
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+ test('adapter can fetch features from volvox.sort.bed.gz simple bed3', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
71
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  var adapter, features, featuresArray, featuresJsonArray;
72
- return _regenerator["default"].wrap(function _callee2$(_context2) {
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+ return _regenerator.default.wrap(function _callee2$(_context2) {
73
73
  while (1) {
74
74
  switch (_context2.prev = _context2.next) {
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  case 0:
76
- adapter = new _BedTabixAdapter["default"](_configSchema["default"].create({
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+ adapter = new _BedTabixAdapter.default(_configSchema.default.create({
77
77
  bedGzLocation: {
78
78
  localPath: require.resolve('./test_data/volvox.sort.bed.gz'),
79
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  locationType: 'LocalPathLocation'
@@ -122,13 +122,13 @@ test('adapter can fetch features from volvox.sort.bed.gz simple bed3', /*#__PURE
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  }
123
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  }, _callee2);
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  })));
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- test('adapter can fetch features bed with autosql', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
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+ test('adapter can fetch features bed with autosql', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
126
126
  var adapter, features, featuresArray, featuresJsonArray;
127
- return _regenerator["default"].wrap(function _callee3$(_context3) {
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+ return _regenerator.default.wrap(function _callee3$(_context3) {
128
128
  while (1) {
129
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  switch (_context3.prev = _context3.next) {
130
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  case 0:
131
- adapter = new _BedTabixAdapter["default"](_configSchema["default"].create({
131
+ adapter = new _BedTabixAdapter.default(_configSchema.default.create({
132
132
  bedGzLocation: {
133
133
  localPath: require.resolve('./test_data/volvox-autosql.bed.gz'),
134
134
  locationType: 'LocalPathLocation'
@@ -178,13 +178,13 @@ test('adapter can fetch features bed with autosql', /*#__PURE__*/(0, _asyncToGen
178
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  }
179
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  }, _callee3);
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  })));
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- test('adapter can fetch bed with header', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4() {
181
+ test('adapter can fetch bed with header', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
182
182
  var adapter, features, featuresArray, featuresJsonArray;
183
- return _regenerator["default"].wrap(function _callee4$(_context4) {
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+ return _regenerator.default.wrap(function _callee4$(_context4) {
184
184
  while (1) {
185
185
  switch (_context4.prev = _context4.next) {
186
186
  case 0:
187
- adapter = new _BedTabixAdapter["default"](_configSchema["default"].create({
187
+ adapter = new _BedTabixAdapter.default(_configSchema.default.create({
188
188
  bedGzLocation: {
189
189
  localPath: require.resolve('./test_data/volvox.sort.with.header.bed.gz'),
190
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  locationType: 'LocalPathLocation'
@@ -233,13 +233,13 @@ test('adapter can fetch bed with header', /*#__PURE__*/(0, _asyncToGenerator2["d
233
233
  }
234
234
  }, _callee4);
235
235
  })));
236
- test('adapter can use gwas header', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5() {
236
+ test('adapter can use gwas header', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
237
237
  var adapter, features, featuresArray, featuresJsonArray;
238
- return _regenerator["default"].wrap(function _callee5$(_context5) {
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+ return _regenerator.default.wrap(function _callee5$(_context5) {
239
239
  while (1) {
240
240
  switch (_context5.prev = _context5.next) {
241
241
  case 0:
242
- adapter = new _BedTabixAdapter["default"](_configSchema["default"].create({
242
+ adapter = new _BedTabixAdapter.default(_configSchema.default.create({
243
243
  bedGzLocation: {
244
244
  localPath: require.resolve('./test_data/gwas.bed.gz'),
245
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  locationType: 'LocalPathLocation'
package/dist/BedTabixAdapter/configSchema.js CHANGED
@@ -3,7 +3,7 @@
3
3
  Object.defineProperty(exports, "__esModule", {
4
4
  value: true
5
5
  });
6
- exports["default"] = void 0;
6
+ exports.default = void 0;
7
7
 
8
8
  var _configuration = require("@jbrowse/core/configuration");
9
9
 
@@ -50,4 +50,4 @@ var _default = (0, _configuration.ConfigurationSchema)('BedTabixAdapter', {
50
50
  explicitlyTyped: true
51
51
  });
52
52
 
53
- exports["default"] = _default;
53
+ exports.default = _default;
package/dist/BedTabixAdapter/index.js CHANGED
@@ -8,7 +8,7 @@ Object.defineProperty(exports, "__esModule", {
8
8
  Object.defineProperty(exports, "configSchema", {
9
9
  enumerable: true,
10
10
  get: function get() {
11
- return _configSchema["default"];
11
+ return _configSchema.default;
12
12
  }
13
13
  });
14
14
 
package/dist/BigBedAdapter/BigBedAdapter.js CHANGED
@@ -5,7 +5,7 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
5
5
  Object.defineProperty(exports, "__esModule", {
6
6
  value: true
7
7
  });
8
- exports["default"] = void 0;
8
+ exports.default = void 0;
9
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10
10
  var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
11
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@@ -50,9 +50,9 @@ var _excluded = ["fields"],
50
50
 
51
51
  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; }
52
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53
- 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; }
53
+ 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; }
54
54
 
55
- 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); }; }
55
+ 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); }; }
56
56
 
57
57
  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; } }
58
58
 
@@ -61,30 +61,30 @@ function isUCSC(f) {
61
61
  }
62
62
 
63
63
  var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
64
- (0, _inherits2["default"])(BigBedAdapter, _BaseFeatureDataAdapt);
64
+ (0, _inherits2.default)(BigBedAdapter, _BaseFeatureDataAdapt);
65
65
 
66
66
  var _super = _createSuper(BigBedAdapter);
67
67
 
68
68
  function BigBedAdapter() {
69
69
  var _this;
70
70
 
71
- (0, _classCallCheck2["default"])(this, BigBedAdapter);
71
+ (0, _classCallCheck2.default)(this, BigBedAdapter);
72
72
 
73
73
  for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
74
74
  args[_key] = arguments[_key];
75
75
  }
76
76
 
77
77
  _this = _super.call.apply(_super, [this].concat(args));
78
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "cached", void 0);
78
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "cached", void 0);
79
79
  return _this;
80
80
  }
81
81
 
82
- (0, _createClass2["default"])(BigBedAdapter, [{
82
+ (0, _createClass2.default)(BigBedAdapter, [{
83
83
  key: "configurePre",
84
84
  value: function () {
85
- var _configurePre = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(opts) {
85
+ var _configurePre = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(opts) {
86
86
  var bigbed, header, parser;
87
- return _regenerator["default"].wrap(function _callee$(_context) {
87
+ return _regenerator.default.wrap(function _callee$(_context) {
88
88
  while (1) {
89
89
  switch (_context.prev = _context.next) {
90
90
  case 0:
@@ -96,7 +96,7 @@ var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
96
96
 
97
97
  case 3:
98
98
  header = _context.sent;
99
- parser = new _bed["default"]({
99
+ parser = new _bed.default({
100
100
  autoSql: header.autoSql
101
101
  });
102
102
  return _context.abrupt("return", {
@@ -122,15 +122,15 @@ var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
122
122
  }, {
123
123
  key: "configure",
124
124
  value: function () {
125
- var _configure = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(opts) {
125
+ var _configure = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(opts) {
126
126
  var _this2 = this;
127
127
 
128
- return _regenerator["default"].wrap(function _callee2$(_context2) {
128
+ return _regenerator.default.wrap(function _callee2$(_context2) {
129
129
  while (1) {
130
130
  switch (_context2.prev = _context2.next) {
131
131
  case 0:
132
132
  if (!this.cached) {
133
- this.cached = this.configurePre(opts)["catch"](function (e) {
133
+ this.cached = this.configurePre(opts).catch(function (e) {
134
134
  _this2.cached = undefined;
135
135
  throw e;
136
136
  });
@@ -155,10 +155,10 @@ var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
155
155
  }, {
156
156
  key: "getRefNames",
157
157
  value: function () {
158
- var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(opts) {
158
+ var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(opts) {
159
159
  var _yield$this$configure, header;
160
160
 
161
- return _regenerator["default"].wrap(function _callee3$(_context3) {
161
+ return _regenerator.default.wrap(function _callee3$(_context3) {
162
162
  while (1) {
163
163
  switch (_context3.prev = _context3.next) {
164
164
  case 0:
@@ -187,10 +187,10 @@ var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
187
187
  }, {
188
188
  key: "getHeader",
189
189
  value: function () {
190
- var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(opts) {
190
+ var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(opts) {
191
191
  var _yield$this$configure2, parser, header, version, fileType, _parser$autoSql, fields, rest;
192
192
 
193
- return _regenerator["default"].wrap(function _callee4$(_context4) {
193
+ return _regenerator.default.wrap(function _callee4$(_context4) {
194
194
  while (1) {
195
195
  switch (_context4.prev = _context4.next) {
196
196
  case 0:
@@ -202,7 +202,7 @@ var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
202
202
  parser = _yield$this$configure2.parser;
203
203
  header = _yield$this$configure2.header;
204
204
  version = header.version, fileType = header.fileType;
205
- _parser$autoSql = parser.autoSql, fields = _parser$autoSql.fields, rest = (0, _objectWithoutProperties2["default"])(_parser$autoSql, _excluded);
205
+ _parser$autoSql = parser.autoSql, fields = _parser$autoSql.fields, rest = (0, _objectWithoutProperties2.default)(_parser$autoSql, _excluded);
206
206
  return _context4.abrupt("return", {
207
207
  version: version,
208
208
  fileType: fileType,
@@ -239,10 +239,10 @@ var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
239
239
  end = region.end;
240
240
  var signal = opts.signal;
241
241
  return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
242
- var _ref2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5(observer) {
242
+ var _ref2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(observer) {
243
243
  var _yield$_this3$configu, parser, bigbed, ob;
244
244
 
245
- return _regenerator["default"].wrap(function _callee5$(_context5) {
245
+ return _regenerator.default.wrap(function _callee5$(_context5) {
246
246
  while (1) {
247
247
  switch (_context5.prev = _context5.next) {
248
248
  case 0:
@@ -296,8 +296,8 @@ var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
296
296
  var chromStart = data.chromStart,
297
297
  chromEnd = data.chromEnd,
298
298
  chrom = data.chrom,
299
- rest = (0, _objectWithoutProperties2["default"])(data, _excluded2);
300
- var f = new _simpleFeature["default"]({
299
+ rest = (0, _objectWithoutProperties2.default)(data, _excluded2);
300
+ var f = new _simpleFeature.default({
301
301
  id: "".concat(_this3.id, "-").concat(r.uniqueId),
302
302
  data: _objectSpread(_objectSpread({}, rest), {}, {
303
303
  start: r.start,
@@ -338,4 +338,4 @@ var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
338
338
  return BigBedAdapter;
339
339
  }(_BaseAdapter.BaseFeatureDataAdapter);
340
340
 
341
- exports["default"] = BigBedAdapter;
341
+ exports.default = BigBedAdapter;
package/dist/BigBedAdapter/BigBedAdapter.test.js CHANGED
@@ -12,13 +12,13 @@ var _BigBedAdapter = _interopRequireDefault(require("./BigBedAdapter"));
12
12
 
13
13
  var _configSchema = _interopRequireDefault(require("./configSchema"));
14
14
 
15
- test('adapter can fetch features from volvox.bb', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
15
+ test('adapter can fetch features from volvox.bb', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
16
16
  var adapter, features, featuresArray, featuresJsonArray;
17
- return _regenerator["default"].wrap(function _callee$(_context) {
17
+ return _regenerator.default.wrap(function _callee$(_context) {
18
18
  while (1) {
19
19
  switch (_context.prev = _context.next) {
20
20
  case 0:
21
- adapter = new _BigBedAdapter["default"](_configSchema["default"].create({
21
+ adapter = new _BigBedAdapter.default(_configSchema.default.create({
22
22
  bigBedLocation: {
23
23
  localPath: require.resolve('./test_data/volvox.bb'),
24
24
  locationType: 'LocalPathLocation'
package/dist/BigBedAdapter/configSchema.js CHANGED
@@ -3,7 +3,7 @@
3
3
  Object.defineProperty(exports, "__esModule", {
4
4
  value: true
5
5
  });
6
- exports["default"] = void 0;
6
+ exports.default = void 0;
7
7
 
8
8
  var _configuration = require("@jbrowse/core/configuration");
9
9
 
@@ -19,4 +19,4 @@ var _default = (0, _configuration.ConfigurationSchema)('BigBedAdapter', {
19
19
  explicitlyTyped: true
20
20
  });
21
21
 
22
- exports["default"] = _default;
22
+ exports.default = _default;
package/dist/BigBedAdapter/index.js CHANGED
@@ -8,7 +8,7 @@ Object.defineProperty(exports, "__esModule", {
8
8
  Object.defineProperty(exports, "configSchema", {
9
9
  enumerable: true,
10
10
  get: function get() {
11
- return _configSchema["default"];
11
+ return _configSchema.default;
12
12
  }
13
13
  });
14
14
 
package/dist/index.js CHANGED
@@ -7,7 +7,7 @@ var _typeof = require("@babel/runtime/helpers/typeof");
7
7
  Object.defineProperty(exports, "__esModule", {
8
8
  value: true
9
9
  });
10
- exports["default"] = void 0;
10
+ exports.default = void 0;
11
11
 
12
12
  var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
13
13
 
@@ -35,43 +35,43 @@ var _tracks = require("@jbrowse/core/util/tracks");
35
35
 
36
36
  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); }
37
37
 
38
- function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
38
+ function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
39
39
 
40
- 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); }; }
40
+ 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); }; }
41
41
 
42
42
  function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
43
43
 
44
44
  var BedPlugin = /*#__PURE__*/function (_Plugin) {
45
- (0, _inherits2["default"])(BedPlugin, _Plugin);
45
+ (0, _inherits2.default)(BedPlugin, _Plugin);
46
46
 
47
47
  var _super = _createSuper(BedPlugin);
48
48
 
49
49
  function BedPlugin() {
50
50
  var _this;
51
51
 
52
- (0, _classCallCheck2["default"])(this, BedPlugin);
52
+ (0, _classCallCheck2.default)(this, BedPlugin);
53
53
 
54
54
  for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
55
55
  args[_key] = arguments[_key];
56
56
  }
57
57
 
58
58
  _this = _super.call.apply(_super, [this].concat(args));
59
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'BedPlugin');
59
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'BedPlugin');
60
60
  return _this;
61
61
  }
62
62
 
63
- (0, _createClass2["default"])(BedPlugin, [{
63
+ (0, _createClass2.default)(BedPlugin, [{
64
64
  key: "install",
65
65
  value: function install(pluginManager) {
66
66
  pluginManager.addAdapterType(function () {
67
- return new _AdapterType["default"]({
67
+ return new _AdapterType.default({
68
68
  name: 'BigBedAdapter',
69
69
  configSchema: _BigBedAdapter.configSchema,
70
70
  getAdapterClass: function getAdapterClass() {
71
71
  return Promise.resolve().then(function () {
72
72
  return _interopRequireWildcard(require('./BigBedAdapter/BigBedAdapter'));
73
73
  }).then(function (r) {
74
- return r["default"];
74
+ return r.default;
75
75
  });
76
76
  }
77
77
  });
@@ -96,14 +96,14 @@ var BedPlugin = /*#__PURE__*/function (_Plugin) {
96
96
  };
97
97
  });
98
98
  pluginManager.addAdapterType(function () {
99
- return new _AdapterType["default"]({
99
+ return new _AdapterType.default({
100
100
  name: 'BedTabixAdapter',
101
101
  configSchema: _BedTabixAdapter.configSchema,
102
102
  getAdapterClass: function getAdapterClass() {
103
103
  return Promise.resolve().then(function () {
104
104
  return _interopRequireWildcard(require('./BedTabixAdapter/BedTabixAdapter'));
105
105
  }).then(function (r) {
106
- return r["default"];
106
+ return r.default;
107
107
  });
108
108
  }
109
109
  });
@@ -132,6 +132,6 @@ var BedPlugin = /*#__PURE__*/function (_Plugin) {
132
132
  }
133
133
  }]);
134
134
  return BedPlugin;
135
- }(_Plugin2["default"]);
135
+ }(_Plugin2.default);
136
136
 
137
- exports["default"] = BedPlugin;
137
+ exports.default = BedPlugin;
package/dist/index.test.js CHANGED
@@ -10,11 +10,11 @@ var _ = _interopRequireDefault(require("."));
10
10
 
11
11
  test('plugin in a stock JBrowse', function () {
12
12
  console.warn = jest.fn();
13
- var pluginManager = new _PluginManager["default"]([new _["default"]()]);
13
+ var pluginManager = new _PluginManager.default([new _.default()]);
14
14
  pluginManager.createPluggableElements();
15
15
  pluginManager.configure();
16
16
  expect(function () {
17
- return pluginManager.addPlugin(new _["default"]());
17
+ return pluginManager.addPlugin(new _.default());
18
18
  }).toThrow(/JBrowse already configured, cannot add plugins/);
19
19
  var BigBedAdapter = pluginManager.getAdapterType('BigBedAdapter');
20
20
  var config = BigBedAdapter.configSchema.create({
package/dist/util.js CHANGED
@@ -116,7 +116,7 @@ function ucscProcessedTranscript(feature) {
116
116
  delete newData.blockCount;
117
117
  delete newData.thickStart;
118
118
  delete newData.thickEnd;
119
- var newFeature = new _simpleFeature["default"]({
119
+ var newFeature = new _simpleFeature.default({
120
120
  data: newData,
121
121
  id: feature.id()
122
122
  });
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-bed",
3
- "version": "1.7.2",
3
+ "version": "1.7.5",
4
4
  "description": "JBrowse 2 bed adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -33,7 +33,8 @@
33
33
  "postbuild": "tsc --build tsconfig.build.json"
34
34
  },
35
35
  "dependencies": {
36
- "@gmod/bbi": "^1.0.32",
36
+ "@babel/runtime": "^7.17.9",
37
+ "@gmod/bbi": "^1.0.35",
37
38
  "@gmod/bed": "^2.0.6",
38
39
  "@gmod/tabix": "^1.5.2"
39
40
  },
@@ -45,5 +46,5 @@
45
46
  "publishConfig": {
46
47
  "access": "public"
47
48
  },
48
- "gitHead": "8710d5770cfebb7351f0a802da2d0c5a0b9e42ba"
49
+ "gitHead": "2c3a1f0c95a47b24eba790eaeb49274caf297aeb"
49
50
  }