@jbrowse/plugin-variants 1.7.0 → 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.
- package/dist/ChordVariantDisplay/index.d.ts +3 -3
- package/dist/ChordVariantDisplay/index.js +3 -3
- package/dist/ChordVariantDisplay/models/ChordVariantDisplay.d.ts +5 -5
- package/dist/ChordVariantDisplay/models/ChordVariantDisplay.js +3 -3
- package/dist/LinearVariantDisplay/configSchema.d.ts +5 -5
- package/dist/LinearVariantDisplay/configSchema.test.js +12 -12
- package/dist/LinearVariantDisplay/index.d.ts +2 -2
- package/dist/LinearVariantDisplay/index.js +1 -1
- package/dist/LinearVariantDisplay/model.d.ts +207 -207
- package/dist/LinearVariantDisplay/model.js +3 -3
- package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts +24 -24
- package/dist/StructuralVariantChordRenderer/ReactComponent.js +17 -17
- package/dist/StructuralVariantChordRenderer/index.d.ts +3 -3
- package/dist/StructuralVariantChordRenderer/index.js +4 -4
- package/dist/VariantFeatureWidget/BreakendOptionDialog.d.ts +10 -10
- package/dist/VariantFeatureWidget/BreakendOptionDialog.js +13 -13
- package/dist/VariantFeatureWidget/VariantFeatureWidget.d.ts +4 -4
- package/dist/VariantFeatureWidget/VariantFeatureWidget.js +32 -32
- package/dist/VariantFeatureWidget/VariantFeatureWidget.test.js +2 -2
- package/dist/VariantFeatureWidget/index.d.ts +11 -11
- package/dist/VcfAdapter/VcfAdapter.d.ts +24 -24
- package/dist/VcfAdapter/VcfAdapter.js +26 -26
- package/dist/VcfAdapter/VcfAdapter.test.js +3 -3
- package/dist/VcfAdapter/configSchema.d.ts +2 -2
- package/dist/VcfAdapter/configSchema.js +2 -2
- package/dist/VcfAdapter/index.d.ts +1 -1
- package/dist/VcfAdapter/index.js +1 -1
- package/dist/VcfTabixAdapter/VcfFeature.d.ts +59 -59
- package/dist/VcfTabixAdapter/VcfFeature.js +19 -19
- package/dist/VcfTabixAdapter/VcfFeature.test.js +14 -14
- package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts +35 -35
- package/dist/VcfTabixAdapter/VcfTabixAdapter.js +26 -26
- package/dist/VcfTabixAdapter/VcfTabixAdapter.test.js +4 -4
- package/dist/VcfTabixAdapter/configSchema.d.ts +2 -2
- package/dist/VcfTabixAdapter/configSchema.js +2 -2
- package/dist/VcfTabixAdapter/index.d.ts +1 -1
- package/dist/VcfTabixAdapter/index.js +1 -1
- package/dist/index.d.ts +7 -7
- package/dist/index.js +19 -19
- package/dist/index.test.js +2 -2
- package/package.json +5 -3
- package/dist/LinearVariantDisplay/configSchema.test.d.ts +0 -1
- package/dist/VariantFeatureWidget/VariantFeatureWidget.test.d.ts +0 -1
- package/dist/index.test.d.ts +0 -1
- package/dist/plugin-variants.cjs.development.js +0 -2897
- package/dist/plugin-variants.cjs.development.js.map +0 -1
- package/dist/plugin-variants.cjs.production.min.js +0 -2
- package/dist/plugin-variants.cjs.production.min.js.map +0 -1
- package/dist/plugin-variants.esm.js +0 -2889
- package/dist/plugin-variants.esm.js.map +0 -1
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Object.defineProperty(exports, "VcfFeature", {
|
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enumerable: true,
|
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get: function get() {
|
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return _VcfFeature
|
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+
return _VcfFeature.default;
|
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}
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});
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-
exports
|
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+
exports.default = void 0;
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|
var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
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@@ -65,43 +65,43 @@ var _VcfFeature = _interopRequireDefault(require("./VcfTabixAdapter/VcfFeature")
|
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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); }
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-
function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return {
|
|
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+
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; }
|
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|
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|
-
function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2
|
|
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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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71
|
|
|
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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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|
var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
|
|
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|
-
(0, _inherits2
|
|
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|
+
(0, _inherits2.default)(VariantsPlugin, _Plugin);
|
|
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76
|
|
|
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|
var _super = _createSuper(VariantsPlugin);
|
|
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|
|
|
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|
function VariantsPlugin() {
|
|
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|
var _this;
|
|
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81
|
|
|
82
|
-
(0, _classCallCheck2
|
|
82
|
+
(0, _classCallCheck2.default)(this, VariantsPlugin);
|
|
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83
|
|
|
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|
for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
|
|
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|
args[_key] = arguments[_key];
|
|
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|
}
|
|
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|
|
|
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|
_this = _super.call.apply(_super, [this].concat(args));
|
|
89
|
-
(0, _defineProperty2
|
|
89
|
+
(0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'VariantsPlugin');
|
|
90
90
|
return _this;
|
|
91
91
|
}
|
|
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92
|
|
|
93
|
-
(0, _createClass2
|
|
93
|
+
(0, _createClass2.default)(VariantsPlugin, [{
|
|
94
94
|
key: "install",
|
|
95
95
|
value: function install(pluginManager) {
|
|
96
96
|
pluginManager.addAdapterType(function () {
|
|
97
|
-
return new _AdapterType
|
|
97
|
+
return new _AdapterType.default({
|
|
98
98
|
name: 'VcfTabixAdapter',
|
|
99
99
|
configSchema: _VcfTabixAdapter.configSchema,
|
|
100
100
|
getAdapterClass: function getAdapterClass() {
|
|
101
101
|
return Promise.resolve().then(function () {
|
|
102
102
|
return _interopRequireWildcard(require('./VcfTabixAdapter/VcfTabixAdapter'));
|
|
103
103
|
}).then(function (r) {
|
|
104
|
-
return r
|
|
104
|
+
return r.default;
|
|
105
105
|
});
|
|
106
106
|
}
|
|
107
107
|
});
|
|
@@ -140,14 +140,14 @@ var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
|
|
|
140
140
|
};
|
|
141
141
|
});
|
|
142
142
|
pluginManager.addAdapterType(function () {
|
|
143
|
-
return new _AdapterType
|
|
143
|
+
return new _AdapterType.default({
|
|
144
144
|
name: 'VcfAdapter',
|
|
145
145
|
configSchema: _VcfAdapter.configSchema,
|
|
146
146
|
getAdapterClass: function getAdapterClass() {
|
|
147
147
|
return Promise.resolve().then(function () {
|
|
148
148
|
return _interopRequireWildcard(require('./VcfAdapter/VcfAdapter'));
|
|
149
149
|
}).then(function (r) {
|
|
150
|
-
return r
|
|
150
|
+
return r.default;
|
|
151
151
|
});
|
|
152
152
|
}
|
|
153
153
|
});
|
|
@@ -169,24 +169,24 @@ var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
|
|
|
169
169
|
};
|
|
170
170
|
});
|
|
171
171
|
pluginManager.addRendererType(function () {
|
|
172
|
-
return pluginManager.jbrequire(_StructuralVariantChordRenderer
|
|
172
|
+
return pluginManager.jbrequire(_StructuralVariantChordRenderer.default);
|
|
173
173
|
});
|
|
174
174
|
pluginManager.addTrackType(function () {
|
|
175
175
|
var configSchema = (0, _configuration.ConfigurationSchema)('VariantTrack', {}, {
|
|
176
176
|
baseConfiguration: (0, _models.createBaseTrackConfig)(pluginManager)
|
|
177
177
|
});
|
|
178
|
-
return new _TrackType
|
|
178
|
+
return new _TrackType.default({
|
|
179
179
|
name: 'VariantTrack',
|
|
180
180
|
configSchema: configSchema,
|
|
181
181
|
stateModel: (0, _models.createBaseTrackModel)(pluginManager, 'VariantTrack', configSchema)
|
|
182
182
|
});
|
|
183
183
|
});
|
|
184
184
|
pluginManager.addDisplayType(function () {
|
|
185
|
-
return pluginManager.jbrequire(_ChordVariantDisplay
|
|
185
|
+
return pluginManager.jbrequire(_ChordVariantDisplay.default);
|
|
186
186
|
});
|
|
187
187
|
pluginManager.addDisplayType(function () {
|
|
188
188
|
var configSchema = (0, _LinearVariantDisplay.configSchemaFactory)(pluginManager);
|
|
189
|
-
return new _DisplayType
|
|
189
|
+
return new _DisplayType.default({
|
|
190
190
|
name: 'LinearVariantDisplay',
|
|
191
191
|
configSchema: configSchema,
|
|
192
192
|
stateModel: (0, _LinearVariantDisplay.modelFactory)(configSchema),
|
|
@@ -196,7 +196,7 @@ var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
|
|
|
196
196
|
});
|
|
197
197
|
});
|
|
198
198
|
pluginManager.addWidgetType(function () {
|
|
199
|
-
return new _WidgetType
|
|
199
|
+
return new _WidgetType.default({
|
|
200
200
|
name: 'VariantFeatureWidget',
|
|
201
201
|
heading: 'Feature details',
|
|
202
202
|
configSchema: _VariantFeatureWidget.configSchema,
|
|
@@ -211,6 +211,6 @@ var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
|
|
|
211
211
|
}
|
|
212
212
|
}]);
|
|
213
213
|
return VariantsPlugin;
|
|
214
|
-
}(_Plugin2
|
|
214
|
+
}(_Plugin2.default);
|
|
215
215
|
|
|
216
|
-
exports
|
|
216
|
+
exports.default = VariantsPlugin;
|
package/dist/index.test.js
CHANGED
|
@@ -14,11 +14,11 @@ var _ = _interopRequireDefault(require("."));
|
|
|
14
14
|
|
|
15
15
|
test('plugin in a stock JBrowse', function () {
|
|
16
16
|
console.warn = jest.fn();
|
|
17
|
-
var pluginManager = new _PluginManager
|
|
17
|
+
var pluginManager = new _PluginManager.default([new _.default(), new _pluginAlignments.default(), new _pluginSvg.default()]);
|
|
18
18
|
pluginManager.createPluggableElements();
|
|
19
19
|
pluginManager.configure();
|
|
20
20
|
expect(function () {
|
|
21
|
-
return pluginManager.addPlugin(new _
|
|
21
|
+
return pluginManager.addPlugin(new _.default());
|
|
22
22
|
}).toThrow(/JBrowse already configured, cannot add plugins/);
|
|
23
23
|
var VcfTabixAdapter = pluginManager.getAdapterType('VcfTabixAdapter');
|
|
24
24
|
var config = VcfTabixAdapter.configSchema.create({
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-variants",
|
|
3
|
-
"version": "1.7.
|
|
3
|
+
"version": "1.7.4",
|
|
4
4
|
"description": "JBrowse 2 variant adapters, tracks, etc.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -29,9 +29,11 @@
|
|
|
29
29
|
"prepack": "yarn build; yarn useDist",
|
|
30
30
|
"postpack": "yarn useSrc",
|
|
31
31
|
"useDist": "node ../../scripts/useDist.js",
|
|
32
|
-
"useSrc": "node ../../scripts/useSrc.js"
|
|
32
|
+
"useSrc": "node ../../scripts/useSrc.js",
|
|
33
|
+
"postbuild": "tsc --build tsconfig.build.json"
|
|
33
34
|
},
|
|
34
35
|
"dependencies": {
|
|
36
|
+
"@babel/runtime": "^7.17.9",
|
|
35
37
|
"@flatten-js/interval-tree": "^1.0.15",
|
|
36
38
|
"@gmod/bgzf-filehandle": "^1.4.3",
|
|
37
39
|
"@gmod/tabix": "^1.5.2",
|
|
@@ -55,5 +57,5 @@
|
|
|
55
57
|
"publishConfig": {
|
|
56
58
|
"access": "public"
|
|
57
59
|
},
|
|
58
|
-
"gitHead": "
|
|
60
|
+
"gitHead": "0a3e0c58055bbab8e3ab0270c139291b96eff403"
|
|
59
61
|
}
|
|
@@ -1 +0,0 @@
|
|
|
1
|
-
export {};
|
|
@@ -1 +0,0 @@
|
|
|
1
|
-
export {};
|
package/dist/index.test.d.ts
DELETED
|
@@ -1 +0,0 @@
|
|
|
1
|
-
export {};
|