@jbrowse/plugin-alignments 1.7.3 → 1.7.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (60) hide show
  1. package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js +26 -26
  2. package/dist/AlignmentsFeatureDetail/index.js +3 -3
  3. package/dist/AlignmentsFeatureDetail/index.test.js +2 -2
  4. package/dist/AlignmentsTrack/index.js +2 -2
  5. package/dist/BamAdapter/BamAdapter.js +31 -31
  6. package/dist/BamAdapter/BamAdapter.test.js +10 -10
  7. package/dist/BamAdapter/BamSlightlyLazyFeature.js +6 -6
  8. package/dist/BamAdapter/MismatchParser.js +6 -6
  9. package/dist/BamAdapter/MismatchParser.test.js +2 -2
  10. package/dist/BamAdapter/configSchema.js +2 -2
  11. package/dist/BamAdapter/index.js +6 -6
  12. package/dist/CramAdapter/CramAdapter.js +31 -31
  13. package/dist/CramAdapter/CramAdapter.test.js +10 -10
  14. package/dist/CramAdapter/CramSlightlyLazyFeature.js +6 -6
  15. package/dist/CramAdapter/CramTestAdapters.js +18 -18
  16. package/dist/CramAdapter/configSchema.js +2 -2
  17. package/dist/CramAdapter/index.js +6 -6
  18. package/dist/HtsgetBamAdapter/HtsgetBamAdapter.js +9 -9
  19. package/dist/HtsgetBamAdapter/configSchema.js +2 -2
  20. package/dist/HtsgetBamAdapter/index.js +6 -6
  21. package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js +8 -8
  22. package/dist/LinearAlignmentsDisplay/index.js +5 -5
  23. package/dist/LinearAlignmentsDisplay/models/configSchema.js +2 -2
  24. package/dist/LinearAlignmentsDisplay/models/configSchema.test.js +11 -11
  25. package/dist/LinearAlignmentsDisplay/models/model.js +15 -15
  26. package/dist/LinearPileupDisplay/components/ColorByModifications.js +18 -18
  27. package/dist/LinearPileupDisplay/components/ColorByTag.js +11 -11
  28. package/dist/LinearPileupDisplay/components/FilterByTag.js +26 -26
  29. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +4 -4
  30. package/dist/LinearPileupDisplay/components/SetFeatureHeight.js +12 -12
  31. package/dist/LinearPileupDisplay/components/SetMaxHeight.js +10 -10
  32. package/dist/LinearPileupDisplay/components/SortByTag.js +10 -10
  33. package/dist/LinearPileupDisplay/configSchema.js +2 -2
  34. package/dist/LinearPileupDisplay/configSchema.test.js +12 -12
  35. package/dist/LinearPileupDisplay/index.js +4 -4
  36. package/dist/LinearPileupDisplay/model.js +22 -22
  37. package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +10 -10
  38. package/dist/LinearSNPCoverageDisplay/index.js +4 -4
  39. package/dist/LinearSNPCoverageDisplay/models/configSchema.js +1 -1
  40. package/dist/LinearSNPCoverageDisplay/models/configSchema.test.js +7 -7
  41. package/dist/LinearSNPCoverageDisplay/models/model.js +11 -11
  42. package/dist/NestedFrequencyTable.js +7 -7
  43. package/dist/PileupRPC/rpcMethods.js +23 -23
  44. package/dist/PileupRenderer/PileupLayoutSession.js +8 -8
  45. package/dist/PileupRenderer/PileupRenderer.js +37 -37
  46. package/dist/PileupRenderer/components/PileupRendering.js +13 -13
  47. package/dist/PileupRenderer/components/PileupRendering.test.js +2 -2
  48. package/dist/PileupRenderer/configSchema.js +2 -2
  49. package/dist/PileupRenderer/index.js +4 -4
  50. package/dist/SNPCoverageAdapter/SNPCoverageAdapter.js +22 -22
  51. package/dist/SNPCoverageAdapter/configSchema.js +2 -2
  52. package/dist/SNPCoverageAdapter/index.js +6 -6
  53. package/dist/SNPCoverageRenderer/SNPCoverageRenderer.js +12 -12
  54. package/dist/SNPCoverageRenderer/configSchema.js +2 -2
  55. package/dist/SNPCoverageRenderer/index.js +3 -3
  56. package/dist/index.js +10 -10
  57. package/dist/index.test.js +2 -2
  58. package/dist/shared.js +5 -5
  59. package/dist/util.js +3 -3
  60. package/package.json +4 -5
@@ -20,7 +20,7 @@ var _SNPCoverageRenderer = _interopRequireDefault(require("../../SNPCoverageRend
20
20
 
21
21
  var _configSchema = _interopRequireDefault(require("./configSchema"));
22
22
 
23
- 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); }; }
23
+ 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); }; }
24
24
 
25
25
  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; } }
26
26
 
@@ -33,26 +33,26 @@ afterEach(function () {
33
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  }); // change renderer
34
34
 
35
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  var SNPCoverageRendererPlugin = /*#__PURE__*/function (_Plugin) {
36
- (0, _inherits2["default"])(SNPCoverageRendererPlugin, _Plugin);
36
+ (0, _inherits2.default)(SNPCoverageRendererPlugin, _Plugin);
37
37
 
38
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  var _super = _createSuper(SNPCoverageRendererPlugin);
39
39
 
40
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  function SNPCoverageRendererPlugin() {
41
- (0, _classCallCheck2["default"])(this, SNPCoverageRendererPlugin);
41
+ (0, _classCallCheck2.default)(this, SNPCoverageRendererPlugin);
42
42
  return _super.apply(this, arguments);
43
43
  }
44
44
 
45
- (0, _createClass2["default"])(SNPCoverageRendererPlugin, [{
45
+ (0, _createClass2.default)(SNPCoverageRendererPlugin, [{
46
46
  key: "install",
47
47
  value: function install(pluginManager) {
48
- (0, _SNPCoverageRenderer["default"])(pluginManager);
48
+ (0, _SNPCoverageRenderer.default)(pluginManager);
49
49
  }
50
50
  }]);
51
51
  return SNPCoverageRendererPlugin;
52
- }(_Plugin2["default"]);
52
+ }(_Plugin2.default);
53
53
 
54
54
  test('has a type attr', function () {
55
- var configSchema = (0, _configSchema["default"])(new _PluginManager["default"]([new SNPCoverageRendererPlugin()]).createPluggableElements().configure());
55
+ var configSchema = (0, _configSchema.default)(new _PluginManager.default([new SNPCoverageRendererPlugin()]).createPluggableElements().configure());
56
56
  var config = configSchema.create({
57
57
  type: 'LinearSNPCoverageDisplay',
58
58
  displayId: 'display1',
@@ -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
9
 
10
10
  var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
11
11
 
@@ -31,7 +31,7 @@ var _shared = require("../../shared");
31
31
 
32
32
  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; }
33
33
 
34
- 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; }
34
+ 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; }
35
35
 
36
36
  // using a map because it preserves order
37
37
  var rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
@@ -39,9 +39,9 @@ var rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
39
39
  var stateModelFactory = function stateModelFactory(pluginManager, configSchema) {
40
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  return _mobxStateTree.types.compose('LinearSNPCoverageDisplay', (0, _pluginWiggle.linearWiggleDisplayModelFactory)(pluginManager, configSchema), _mobxStateTree.types.model({
41
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  type: _mobxStateTree.types.literal('LinearSNPCoverageDisplay'),
42
- drawInterbaseCounts: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
43
- drawIndicators: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
44
- drawArcs: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
42
+ drawInterbaseCounts: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
43
+ drawIndicators: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
44
+ drawArcs: _mobxStateTree.types.maybe(_mobxStateTree.types.boolean),
45
45
  filterBy: _mobxStateTree.types.optional(_mobxStateTree.types.model({
46
46
  flagInclude: _mobxStateTree.types.optional(_mobxStateTree.types.number, 0),
47
47
  flagExclude: _mobxStateTree.types.optional(_mobxStateTree.types.number, 1540),
@@ -55,7 +55,7 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
55
55
  type: _mobxStateTree.types.string,
56
56
  tag: _mobxStateTree.types.maybe(_mobxStateTree.types.string)
57
57
  }))
58
- }))["volatile"](function () {
58
+ })).volatile(function () {
59
59
  return {
60
60
  modificationTagMap: _mobx.observable.map({})
61
61
  };
@@ -135,10 +135,10 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
135
135
  self.drawArcs = !self.drawArcsSetting;
136
136
  },
137
137
  afterAttach: function afterAttach() {
138
- (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
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+ (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
139
139
  var colorBy, _ref2, staticBlocks, vals;
140
140
 
141
- return _regenerator["default"].wrap(function _callee$(_context) {
141
+ return _regenerator.default.wrap(function _callee$(_context) {
142
142
  while (1) {
143
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  switch (_context.prev = _context.next) {
144
144
  case 0:
@@ -183,7 +183,7 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
183
183
  var superTrackMenuItems = self.trackMenuItems;
184
184
  return {
185
185
  get TooltipComponent() {
186
- return _Tooltip["default"];
186
+ return _Tooltip.default;
187
187
  },
188
188
 
189
189
  get adapterConfig() {
@@ -206,7 +206,7 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
206
206
  return [];
207
207
  },
208
208
  trackMenuItems: function trackMenuItems() {
209
- return [].concat((0, _toConsumableArray2["default"])(superTrackMenuItems()), [{
209
+ return [].concat((0, _toConsumableArray2.default)(superTrackMenuItems()), [{
210
210
  label: 'Draw insertion/clipping indicators',
211
211
  type: 'checkbox',
212
212
  checked: self.drawIndicatorsSetting,
@@ -234,4 +234,4 @@ var stateModelFactory = function stateModelFactory(pluginManager, configSchema)
234
234
  };
235
235
 
236
236
  var _default = stateModelFactory;
237
- exports["default"] = _default;
237
+ exports.default = _default;
@@ -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
9
 
10
10
  var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
11
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@@ -15,7 +15,7 @@ var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/de
15
15
 
16
16
  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; }
17
17
 
18
- 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; }
18
+ 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; }
19
19
 
20
20
  /* eslint-disable @typescript-eslint/no-explicit-any */
21
21
  // see perf results on object.keys vs for-in loop
@@ -23,13 +23,13 @@ function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { va
23
23
  var NestedFrequencyTable = /*#__PURE__*/function () {
24
24
  function NestedFrequencyTable() {
25
25
  var initialData = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
26
- (0, _classCallCheck2["default"])(this, NestedFrequencyTable);
27
- (0, _defineProperty2["default"])(this, "categories", void 0);
26
+ (0, _classCallCheck2.default)(this, NestedFrequencyTable);
27
+ (0, _defineProperty2.default)(this, "categories", void 0);
28
28
  this.categories = _objectSpread({}, initialData);
29
29
  } // get the sum of all the category counts
30
30
 
31
31
 
32
- (0, _createClass2["default"])(NestedFrequencyTable, [{
32
+ (0, _createClass2.default)(NestedFrequencyTable, [{
33
33
  key: "total",
34
34
  value: function total() {
35
35
  // calculate total if necessary
@@ -104,7 +104,7 @@ var NestedFrequencyTable = /*#__PURE__*/function () {
104
104
 
105
105
  if (!slot || !slot.categories) {
106
106
  this.categories[slotName] = new NestedFrequencyTable(slot ? {
107
- "default": slot + 0
107
+ default: slot + 0
108
108
  } : {});
109
109
  }
110
110
 
@@ -149,4 +149,4 @@ var NestedFrequencyTable = /*#__PURE__*/function () {
149
149
  return NestedFrequencyTable;
150
150
  }();
151
151
 
152
- exports["default"] = NestedFrequencyTable;
152
+ exports.default = NestedFrequencyTable;
@@ -41,37 +41,37 @@ var _util2 = require("../util");
41
41
 
42
42
  var _MismatchParser = require("../BamAdapter/MismatchParser");
43
43
 
44
- 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); }; }
44
+ 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); }; }
45
45
 
46
46
  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; } }
47
47
 
48
48
  var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
49
- (0, _inherits2["default"])(PileupGetGlobalValueForTag, _RpcMethodType);
49
+ (0, _inherits2.default)(PileupGetGlobalValueForTag, _RpcMethodType);
50
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51
51
  var _super = _createSuper(PileupGetGlobalValueForTag);
52
52
 
53
53
  function PileupGetGlobalValueForTag() {
54
54
  var _this;
55
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56
- (0, _classCallCheck2["default"])(this, PileupGetGlobalValueForTag);
56
+ (0, _classCallCheck2.default)(this, PileupGetGlobalValueForTag);
57
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58
58
  for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
59
59
  args[_key] = arguments[_key];
60
60
  }
61
61
 
62
62
  _this = _super.call.apply(_super, [this].concat(args));
63
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "name", 'PileupGetGlobalValueForTag');
63
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'PileupGetGlobalValueForTag');
64
64
  return _this;
65
65
  }
66
66
 
67
- (0, _createClass2["default"])(PileupGetGlobalValueForTag, [{
67
+ (0, _createClass2.default)(PileupGetGlobalValueForTag, [{
68
68
  key: "serializeArguments",
69
69
  value: function () {
70
- var _serializeArguments = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(args, rpcDriverClassName) {
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+ var _serializeArguments = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(args, rpcDriverClassName) {
71
71
  var _rootModel$session;
72
72
 
73
73
  var rootModel, assemblyManager, renamedArgs;
74
- return _regenerator["default"].wrap(function _callee$(_context) {
74
+ return _regenerator.default.wrap(function _callee$(_context) {
75
75
  while (1) {
76
76
  switch (_context.prev = _context.next) {
77
77
  case 0:
@@ -91,7 +91,7 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
91
91
 
92
92
  case 6:
93
93
  renamedArgs = _context.sent;
94
- return _context.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupGetGlobalValueForTag.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
94
+ return _context.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(PileupGetGlobalValueForTag.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
95
95
 
96
96
  case 8:
97
97
  case "end":
@@ -110,9 +110,9 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
110
110
  }, {
111
111
  key: "execute",
112
112
  value: function () {
113
- var _execute = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(args, rpcDriverClassName) {
113
+ var _execute = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(args, rpcDriverClassName) {
114
114
  var deserializedArgs, adapterConfig, sessionId, regions, tag, dataAdapter, features, featuresArray, uniqueValues;
115
- return _regenerator["default"].wrap(function _callee2$(_context2) {
115
+ return _regenerator.default.wrap(function _callee2$(_context2) {
116
116
  while (1) {
117
117
  switch (_context2.prev = _context2.next) {
118
118
  case 0:
@@ -142,7 +142,7 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
142
142
  uniqueValues.add("".concat(val));
143
143
  }
144
144
  });
145
- return _context2.abrupt("return", (0, _toConsumableArray2["default"])(uniqueValues));
145
+ return _context2.abrupt("return", (0, _toConsumableArray2.default)(uniqueValues));
146
146
 
147
147
  case 14:
148
148
  case "end":
@@ -160,37 +160,37 @@ var PileupGetGlobalValueForTag = /*#__PURE__*/function (_RpcMethodType) {
160
160
  }()
161
161
  }]);
162
162
  return PileupGetGlobalValueForTag;
163
- }(_RpcMethodType3["default"]);
163
+ }(_RpcMethodType3.default);
164
164
 
165
165
  exports.PileupGetGlobalValueForTag = PileupGetGlobalValueForTag;
166
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167
167
  var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
168
- (0, _inherits2["default"])(PileupGetVisibleModifications, _RpcMethodType2);
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+ (0, _inherits2.default)(PileupGetVisibleModifications, _RpcMethodType2);
169
169
 
170
170
  var _super2 = _createSuper(PileupGetVisibleModifications);
171
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172
172
  function PileupGetVisibleModifications() {
173
173
  var _this2;
174
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175
- (0, _classCallCheck2["default"])(this, PileupGetVisibleModifications);
175
+ (0, _classCallCheck2.default)(this, PileupGetVisibleModifications);
176
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177
177
  for (var _len2 = arguments.length, args = new Array(_len2), _key2 = 0; _key2 < _len2; _key2++) {
178
178
  args[_key2] = arguments[_key2];
179
179
  }
180
180
 
181
181
  _this2 = _super2.call.apply(_super2, [this].concat(args));
182
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this2), "name", 'PileupGetVisibleModifications');
182
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this2), "name", 'PileupGetVisibleModifications');
183
183
  return _this2;
184
184
  }
185
185
 
186
- (0, _createClass2["default"])(PileupGetVisibleModifications, [{
186
+ (0, _createClass2.default)(PileupGetVisibleModifications, [{
187
187
  key: "serializeArguments",
188
188
  value: function () {
189
- var _serializeArguments2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(args, rpcDriverClassName) {
189
+ var _serializeArguments2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(args, rpcDriverClassName) {
190
190
  var _rootModel$session2;
191
191
 
192
192
  var rootModel, assemblyManager, renamedArgs;
193
- return _regenerator["default"].wrap(function _callee3$(_context3) {
193
+ return _regenerator.default.wrap(function _callee3$(_context3) {
194
194
  while (1) {
195
195
  switch (_context3.prev = _context3.next) {
196
196
  case 0:
@@ -210,7 +210,7 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
210
210
 
211
211
  case 6:
212
212
  renamedArgs = _context3.sent;
213
- return _context3.abrupt("return", (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupGetVisibleModifications.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
213
+ return _context3.abrupt("return", (0, _get2.default)((0, _getPrototypeOf2.default)(PileupGetVisibleModifications.prototype), "serializeArguments", this).call(this, renamedArgs, rpcDriverClassName));
214
214
 
215
215
  case 8:
216
216
  case "end":
@@ -229,9 +229,9 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
229
229
  }, {
230
230
  key: "execute",
231
231
  value: function () {
232
- var _execute2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(args, rpcDriverClassName) {
232
+ var _execute2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(args, rpcDriverClassName) {
233
233
  var deserializedArgs, adapterConfig, sessionId, regions, dataAdapter, features, featuresArray, uniqueValues;
234
- return _regenerator["default"].wrap(function _callee4$(_context4) {
234
+ return _regenerator.default.wrap(function _callee4$(_context4) {
235
235
  while (1) {
236
236
  switch (_context4.prev = _context4.next) {
237
237
  case 0:
@@ -262,7 +262,7 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
262
262
  });
263
263
  }
264
264
  });
265
- return _context4.abrupt("return", (0, _toConsumableArray2["default"])(uniqueValues));
265
+ return _context4.abrupt("return", (0, _toConsumableArray2.default)(uniqueValues));
266
266
 
267
267
  case 14:
268
268
  case "end":
@@ -280,6 +280,6 @@ var PileupGetVisibleModifications = /*#__PURE__*/function (_RpcMethodType2) {
280
280
  }()
281
281
  }]);
282
282
  return PileupGetVisibleModifications;
283
- }(_RpcMethodType3["default"]);
283
+ }(_RpcMethodType3.default);
284
284
 
285
285
  exports.PileupGetVisibleModifications = PileupGetVisibleModifications;
@@ -29,33 +29,33 @@ var _BoxRendererType = require("@jbrowse/core/pluggableElementTypes/renderers/Bo
29
29
 
30
30
  var _configuration = require("@jbrowse/core/configuration");
31
31
 
32
- 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); }; }
32
+ 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); }; }
33
33
 
34
34
  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; } }
35
35
 
36
36
  // Sorting and revealing soft clip changes the layout of Pileup renderer
37
37
  // Adds extra conditions to see if cached layout is valid
38
38
  var PileupLayoutSession = /*#__PURE__*/function (_LayoutSession) {
39
- (0, _inherits2["default"])(PileupLayoutSession, _LayoutSession);
39
+ (0, _inherits2.default)(PileupLayoutSession, _LayoutSession);
40
40
 
41
41
  var _super = _createSuper(PileupLayoutSession);
42
42
 
43
43
  function PileupLayoutSession(args) {
44
44
  var _this;
45
45
 
46
- (0, _classCallCheck2["default"])(this, PileupLayoutSession);
46
+ (0, _classCallCheck2.default)(this, PileupLayoutSession);
47
47
  _this = _super.call(this, args);
48
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "sortedBy", void 0);
49
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "showSoftClip", false);
50
- (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "cachedLayout", void 0);
48
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "sortedBy", void 0);
49
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "showSoftClip", false);
50
+ (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "cachedLayout", void 0);
51
51
  _this.config = args.config;
52
52
  return _this;
53
53
  }
54
54
 
55
- (0, _createClass2["default"])(PileupLayoutSession, [{
55
+ (0, _createClass2.default)(PileupLayoutSession, [{
56
56
  key: "cachedLayoutIsValid",
57
57
  value: function cachedLayoutIsValid(cachedLayout) {
58
- return (0, _get2["default"])((0, _getPrototypeOf2["default"])(PileupLayoutSession.prototype), "cachedLayoutIsValid", this).call(this, cachedLayout) && this.showSoftClip === cachedLayout.showSoftClip && (0, _fastDeepEqual["default"])(this.sortedBy, cachedLayout.sortedBy);
58
+ return (0, _get2.default)((0, _getPrototypeOf2.default)(PileupLayoutSession.prototype), "cachedLayoutIsValid", this).call(this, cachedLayout) && this.showSoftClip === cachedLayout.showSoftClip && (0, _fastDeepEqual.default)(this.sortedBy, cachedLayout.sortedBy);
59
59
  }
60
60
  }, {
61
61
  key: "layout",