@jbrowse/plugin-variants 2.4.0 → 2.4.2

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Files changed (41) hide show
  1. package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts +5 -2
  2. package/dist/ChordVariantDisplay/models/stateModelFactory.js +1 -1
  3. package/dist/ChordVariantDisplay/models/stateModelFactory.js.map +1 -1
  4. package/dist/LinearVariantDisplay/model.d.ts +25 -28
  5. package/dist/LinearVariantDisplay/model.js.map +1 -1
  6. package/dist/VariantFeatureWidget/BreakendOptionDialog.js +4 -3
  7. package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
  8. package/dist/VariantFeatureWidget/index.d.ts +1 -1
  9. package/dist/VcfAdapter/VcfAdapter.d.ts +3 -1
  10. package/dist/VcfAdapter/VcfAdapter.js +9 -10
  11. package/dist/VcfAdapter/VcfAdapter.js.map +1 -1
  12. package/dist/VcfFeature/index.js +1 -1
  13. package/dist/VcfFeature/index.js.map +1 -1
  14. package/dist/VcfFeature/util.js +4 -7
  15. package/dist/VcfFeature/util.js.map +1 -1
  16. package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts +1 -1
  17. package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts +5 -2
  18. package/esm/ChordVariantDisplay/models/stateModelFactory.js +1 -1
  19. package/esm/ChordVariantDisplay/models/stateModelFactory.js.map +1 -1
  20. package/esm/LinearVariantDisplay/model.d.ts +25 -28
  21. package/esm/LinearVariantDisplay/model.js.map +1 -1
  22. package/esm/VariantFeatureWidget/BreakendOptionDialog.js +4 -3
  23. package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map +1 -1
  24. package/esm/VariantFeatureWidget/index.d.ts +1 -1
  25. package/esm/VcfAdapter/VcfAdapter.d.ts +3 -1
  26. package/esm/VcfAdapter/VcfAdapter.js +9 -10
  27. package/esm/VcfAdapter/VcfAdapter.js.map +1 -1
  28. package/esm/VcfFeature/index.js +1 -1
  29. package/esm/VcfFeature/index.js.map +1 -1
  30. package/esm/VcfFeature/util.js +4 -7
  31. package/esm/VcfFeature/util.js.map +1 -1
  32. package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts +1 -1
  33. package/package.json +3 -3
  34. package/src/ChordVariantDisplay/models/stateModelFactory.ts +2 -2
  35. package/src/LinearVariantDisplay/model.ts +10 -4
  36. package/src/VariantFeatureWidget/BreakendOptionDialog.tsx +11 -5
  37. package/src/VariantFeatureWidget/VariantFeatureWidget.test.tsx +1 -1
  38. package/src/VcfAdapter/VcfAdapter.ts +15 -16
  39. package/src/VcfFeature/index.ts +1 -1
  40. package/src/VcfFeature/util.ts +4 -6
  41. package/src/VcfTabixAdapter/__snapshots__/VcfTabixAdapter.test.ts.snap +5 -5
package/dist/ChordVariantDisplay/models/stateModelFactory.d.ts CHANGED
@@ -1,5 +1,6 @@
1
1
  /// <reference types="react" />
2
2
  import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
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+ import { Feature } from '@jbrowse/core/util';
3
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  /**
4
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  * #stateModel ChordVariantDisplay
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  * extends `BaseChordDisplay`
@@ -22,7 +23,9 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
22
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  configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
23
24
  }, {
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  rendererTypeName: string;
25
- error: unknown;
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+ error: unknown; /**
27
+ * #property
28
+ */
26
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  } & {
27
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  readonly RenderingComponent: import("react").FC<{
28
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  model: {
@@ -81,7 +84,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
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  renderingComponent: import("@jbrowse/core/util").AnyReactComponentType | undefined;
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  refNameMap: Record<string, string> | undefined;
83
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  } & {
84
- onChordClick(feature: import("@jbrowse/core/util").Feature): void;
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+ onChordClick(feature: Feature): void;
85
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  } & {
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  readonly blockDefinitions: import("@jbrowse/plugin-circular-view/src/CircularView/models/slices").Slice[];
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  renderProps(): any;
package/dist/ChordVariantDisplay/models/stateModelFactory.js CHANGED
@@ -41,7 +41,7 @@ const stateModelFactory = (configSchema) => {
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  radius: view.radiusPx,
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  blockDefinitions: self.blockDefinitions,
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  config: self.configuration.renderer,
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- onChordClick: self.onChordClick,
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+ onChordClick: (arg) => self.onChordClick(arg),
45
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  };
46
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  },
47
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  }));
package/dist/ChordVariantDisplay/models/stateModelFactory.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"stateModelFactory.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/stateModelFactory.ts"],"names":[],"mappings":";;AAAA,wEAAqE;AACrE,+DAGoC;AACpC,qDAAuC;AACvC,6CAAsD;AACtD,sDAAgE;AAEhE;;;GAGG;AACH,MAAM,iBAAiB,GAAG,CAAC,YAAwC,EAAE,EAAE;IACrE,OAAO,uBAAK;SACT,OAAO,CACN,qBAAqB,EACrB,4CAAqB,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,WAAW;YACT,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;YACpC,OAAO;gBACL,GAAG,IAAA,6BAAoB,EAAC,IAAI,CAAC;gBAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;gBACjC,YAAY,EAAE,IAAI;gBAClB,YAAY,EAAE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,iBAAiB;gBACpD,MAAM,EAAE,IAAI,CAAC,QAAQ;gBACrB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;gBACnC,YAAY,EAAE,IAAI,CAAC,YAAY;aAChC,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,kBAAe,iBAAiB,CAAA"}
1
+ {"version":3,"file":"stateModelFactory.js","sourceRoot":"","sources":["../../../src/ChordVariantDisplay/models/stateModelFactory.ts"],"names":[],"mappings":";;AAAA,wEAAqE;AACrE,+DAGoC;AACpC,qDAAuC;AACvC,6CAA+D;AAC/D,sDAAgE;AAEhE;;;GAGG;AACH,MAAM,iBAAiB,GAAG,CAAC,YAAwC,EAAE,EAAE;IACrE,OAAO,uBAAK;SACT,OAAO,CACN,qBAAqB,EACrB,4CAAqB,EACrB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,qBAAqB,CAAC;QAC1C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;QAED;;WAEG;QACH,WAAW;YACT,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;YACpC,OAAO;gBACL,GAAG,IAAA,6BAAoB,EAAC,IAAI,CAAC;gBAC7B,aAAa,EAAE,IAAI,CAAC,aAAa;gBACjC,YAAY,EAAE,IAAI;gBAClB,YAAY,EAAE,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,iBAAiB;gBACpD,MAAM,EAAE,IAAI,CAAC,QAAQ;gBACrB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;gBACnC,YAAY,EAAE,CAAC,GAAY,EAAE,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC;aACvD,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC,CAAA;AAED,0EAA0E;AAE1E,wDAAwD;AAExD,2BAA2B;AAC3B,EAAE;AACF,kBAAe,iBAAiB,CAAA"}
package/dist/LinearVariantDisplay/model.d.ts CHANGED
@@ -1,12 +1,13 @@
1
1
  /// <reference types="react" />
2
- import { Feature } from '@jbrowse/core/util/simpleFeature';
3
- import { LinearVariantDisplayConfigModel } from './configSchema';
2
+ import { Feature } from '@jbrowse/core/util';
3
+ import { Instance } from 'mobx-state-tree';
4
+ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
4
5
  /**
5
6
  * #stateModel LinearVariantDisplay
6
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  * extends `LinearBasicDisplay`
7
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  * very similar to basic display, but provides custom widget on feature click
8
9
  */
9
- export default function stateModelFactory(configSchema: LinearVariantDisplayConfigModel): import("mobx-state-tree").IModelType<{
10
+ export default function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
10
11
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
11
12
  type: import("mobx-state-tree").ISimpleType<string>;
12
13
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -63,7 +64,9 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
63
64
  } & {
64
65
  type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
65
66
  trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
66
- trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
67
+ trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
68
+ * #action
69
+ */
67
70
  trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
68
71
  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
69
72
  configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
@@ -134,10 +137,10 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
134
137
  message: string;
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138
  featureIdUnderMouse: string | undefined;
136
139
  contextMenuFeature: Feature | undefined;
137
- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
138
- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
140
+ estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
141
+ estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
139
142
  } & {
140
- readonly height: any;
143
+ readonly height: number;
141
144
  readonly blockType: "dynamicBlocks" | "staticBlocks";
142
145
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
143
146
  } & {
@@ -148,7 +151,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
148
151
  } & {
149
152
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
150
153
  readonly featureUnderMouse: Feature | undefined;
151
- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
154
+ getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
152
155
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
153
156
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
154
157
  readonly currentBytesRequested: number;
@@ -158,19 +161,16 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
158
161
  readonly maxAllowableBytes: number;
159
162
  } & {
160
163
  setMessage(message: string): void;
164
+ } & {
161
165
  afterAttach(): void;
162
- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
163
- headers?: Record<string, string> | undefined;
164
- signal?: AbortSignal | undefined;
165
- filters?: string[] | undefined;
166
- }): Promise<{}>;
167
- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
168
- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
169
- clearRegionStats(): void;
170
- setHeight(displayHeight: number): any;
166
+ estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
167
+ setRegionsStatsP(arg: any): void;
168
+ setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
169
+ clearRegionsStats(): void;
170
+ setHeight(displayHeight: number): number;
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171
  resizeHeight(distance: number): number;
172
172
  setScrollTop(scrollTop: number): void;
173
- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
173
+ updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
174
174
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
175
175
  setCurrBpPerPx(n: number): void;
176
176
  deleteBlock(key: string): void;
@@ -184,18 +184,13 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
184
184
  readonly regionTooLargeReason: string;
185
185
  } & {
186
186
  reload(): Promise<void>;
187
+ } & {
187
188
  afterAttach(): void;
188
189
  } & {
189
190
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
190
191
  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
191
192
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
192
- contextMenuItems(): {
193
- label: string;
194
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
195
- muiName: string;
196
- };
197
- onClick: () => void;
198
- }[];
193
+ contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
199
194
  renderProps(): any;
200
195
  } & {
201
196
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -213,19 +208,19 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
213
208
  [x: string]: any;
214
209
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
215
210
  setSubschema(slotName: string, data: unknown): any;
216
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
211
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
217
212
  } & {
218
213
  toggleShowLabels(): void;
219
214
  toggleShowDescriptions(): void;
220
215
  setDisplayMode(val: string): void;
221
- setMaxHeight(val: number): void;
216
+ setMaxHeight(val?: number | undefined): void;
222
217
  } & {
223
218
  renderProps(): {
224
219
  config: {
225
220
  [x: string]: any;
226
221
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
227
222
  setSubschema(slotName: string, data: unknown): any;
228
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
223
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
229
224
  };
230
225
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
231
226
  } & {
@@ -234,3 +229,5 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
234
229
  */
235
230
  selectFeature(feature: Feature): Promise<void>;
236
231
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
232
+ export type LinearVariantDisplayStateModel = ReturnType<typeof stateModelFactory>;
233
+ export type LinearVariantDisplayModel = Instance<LinearVariantDisplayStateModel>;
package/dist/LinearVariantDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":";;AAAA,+DAA6E;AAC7E,sDAA2D;AAC3D,6CAK2B;AAG3B,kFAAmF;AACnF,qDAAuC;AAGvC;;;;GAIG;AACH,SAAwB,iBAAiB,CACvC,YAA6C;IAE7C,OAAO,uBAAK;SACT,OAAO,CACN,sBAAsB,EACtB,IAAA,0DAA8B,EAAC,YAAY,CAAC,EAC5C,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SACA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI,IAAA,gCAAyB,EAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,YAAY,GAAG,MAAM,UAAU,CAAC,IAAI,CACxC,SAAS,EACT,iBAAiB,EACjB;oBACE,aAAa;iBACd,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,sBAAsB,EAAE,gBAAgB,EAAE;oBAC1D,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI;oBACJ,KAAK;oBACL,YAAY;iBACb,CAAC,CACH,CAAA;aACF;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAlDD,oCAkDC"}
1
+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":";;AAAA,+DAA6E;AAC7E,sDAA2D;AAC3D,6CAM2B;AAE3B,kFAAmF;AACnF,qDAAiD;AAGjD;;;;GAIG;AACH,SAAwB,iBAAiB,CACvC,YAAwC;IAExC,OAAO,uBAAK;SACT,OAAO,CACN,sBAAsB,EACtB,IAAA,0DAA8B,EAAC,YAAY,CAAC,EAC5C,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;KACpD,CAAC,CACH;SAEA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAI,IAAA,gCAAyB,EAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,IAAA,yBAAkB,EAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,YAAY,GAAG,MAAM,UAAU,CAAC,IAAI,CACxC,SAAS,EACT,iBAAiB,EACjB;oBACE,aAAa;iBACd,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,sBAAsB,EAAE,gBAAgB,EAAE;oBAC1D,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI;oBACJ,KAAK;oBACL,YAAY;iBACb,CAAC,CACH,CAAA;aACF;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC;AAnDD,oCAmDC"}
package/dist/VariantFeatureWidget/BreakendOptionDialog.js CHANGED
@@ -52,17 +52,18 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
52
52
  try {
53
53
  const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
54
54
  function remapIds(arr) {
55
- return arr.map((v) => ({
55
+ return arr.map(v => ({
56
56
  ...v,
57
- id: v.trackId + '-' + Math.random(),
57
+ id: `${v.trackId}-${Math.random()}`,
58
58
  }));
59
59
  }
60
60
  viewSnapshot.views[0].offsetPx -= view.width / 2 + 100;
61
61
  viewSnapshot.views[1].offsetPx -= view.width / 2 + 100;
62
62
  viewSnapshot.featureData = feature;
63
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
63
64
  const viewTracks = (0, mobx_state_tree_1.getSnapshot)(view.tracks);
64
65
  viewSnapshot.views[0].tracks = remapIds(viewTracks);
65
- viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? viewTracks.slice().reverse() : viewTracks);
66
+ viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? [...viewTracks].reverse() : viewTracks);
66
67
  session.addView('BreakpointSplitView', viewSnapshot);
67
68
  }
68
69
  catch (e) {
package/dist/VariantFeatureWidget/BreakendOptionDialog.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uDAAuD;AACvD,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,uCAA0C;AAC1C,qDAA6C;AAC7C,UAAU;AACV,yCAAyC;AACzC,6CAAwD;AAExD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAA;AAEF,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,8BAAC,wBAAa;YACZ,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBACD,SAAS,QAAQ,CAAC,GAAU;4BAC1B,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC;gCAC1B,GAAG,CAAC;gCACJ,EAAE,EAAE,CAAC,CAAC,OAAO,GAAG,GAAG,GAAG,IAAI,CAAC,MAAM,EAAE;6BACpC,CAAC,CAAC,CAAA;wBACL,CAAC;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,MAAM,UAAU,GAAG,IAAA,6BAAW,EAAC,IAAI,CAAC,MAAM,CAAc,CAAA;wBACxD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;wBACnD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CACrC,YAAY,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,UAAU,CACzD,CAAA;wBAED,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,oBAAoB,CAAC,CAAA"}
1
+ {"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uDAAuD;AACvD,+CAAuC;AACvC,2CAAqC;AACrC,4CAMsB;AACtB,uCAA0C;AAC1C,qDAA6C;AAC7C,UAAU;AACV,yCAAyC;AACzC,6CAAwD;AAExD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAA;AAEF,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,IAAA,gBAAQ,EAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,8BAAC,WAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,8BAAC,wBAAa;YACZ,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,8BAAC,2BAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,8BAAC,mBAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,8BAAC,wBAAa;YACZ,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBAMD,SAAS,QAAQ,CAAC,GAAY;4BAC5B,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;gCACnB,GAAG,CAAC;gCACJ,EAAE,EAAE,GAAG,CAAC,CAAC,OAAO,IAAI,IAAI,CAAC,MAAM,EAAE,EAAE;6BACpC,CAAC,CAAC,CAAA;wBACL,CAAC;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,4EAA4E;wBAC5E,MAAM,UAAU,GAAG,IAAA,6BAAW,EAAC,IAAI,CAAC,MAAM,CAAY,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;wBACnD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CACrC,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,UAAU,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,UAAU,CACtD,CAAA;wBAED,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,8BAAC,iBAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,oBAAoB,CAAC,CAAA"}
package/dist/VariantFeatureWidget/index.d.ts CHANGED
@@ -33,8 +33,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
33
33
  trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
34
34
  trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
35
35
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
36
- id: string;
37
36
  type: "BaseFeatureWidget";
37
+ id: string;
38
38
  track: import("mobx-state-tree").ReferenceIdentifier | undefined;
39
39
  view: import("mobx-state-tree").ReferenceIdentifier | undefined;
40
40
  trackId: string | undefined;
package/dist/VcfAdapter/VcfAdapter.d.ts CHANGED
@@ -11,7 +11,9 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
11
11
  getMetadata(): Promise<any>;
12
12
  setupP(): Promise<{
13
13
  header: string;
14
- intervalTree: Record<string, IntervalTree<any>>;
14
+ intervalTree: {
15
+ [key: string]: IntervalTree<any>;
16
+ };
15
17
  }>;
16
18
  setup(): Promise<{
17
19
  header: string;
package/dist/VcfAdapter/VcfAdapter.js CHANGED
@@ -51,22 +51,21 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
51
51
  }
52
52
  const str = new TextDecoder().decode(buffer);
53
53
  const { header, lines } = readVcf(str);
54
- const intervalTree = lines
55
- .map((line, id) => {
54
+ const intervalTree = {};
55
+ for (const obj of lines.map((line, id) => {
56
56
  var _a;
57
57
  const [refName, startP, , ref, , , , info] = line.split('\t');
58
58
  const start = +startP - 1;
59
- const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || start + ref.length);
59
+ const def = start + ref.length;
60
+ const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || def);
60
61
  return { line, refName, start, end, id };
61
- })
62
- .reduce((acc, obj) => {
62
+ })) {
63
63
  const key = obj.refName;
64
- if (!acc[key]) {
65
- acc[key] = new interval_tree_1.default();
64
+ if (!intervalTree[key]) {
65
+ intervalTree[key] = new interval_tree_1.default();
66
66
  }
67
- acc[key].insert([obj.start, obj.end], obj);
68
- return acc;
69
- }, {});
67
+ intervalTree[key].insert([obj.start, obj.end], obj);
68
+ }
70
69
  return { header, intervalTree };
71
70
  }
72
71
  async setup() {
package/dist/VcfAdapter/VcfAdapter.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,8EAAoD;AACpD,2DAA6C;AAC7C,oDAA2B;AAE3B,QAAQ;AACR,+DAAsC;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QAEtC,MAAM,YAAY,GAAG,KAAK;aACvB,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YAChB,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,CAAA;YACxE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC;aACD,MAAM,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;gBACb,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;aAC9B;YACD,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;YAC1C,OAAO,GAAG,CAAA;QACZ,CAAC,EAAE,EAAkC,CAAC,CAAA;QAExC,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AA1FjC,6BA2FC;AA1Fe,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}
1
+ {"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":";;;;;AAAA,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,8EAAoD;AACpD,2DAA6C;AAC7C,oDAA2B;AAE3B,QAAQ;AACR,+DAAsC;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAqB,UAAW,SAAQ,oCAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAA,iBAAY,EAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QACtC,MAAM,YAAY,GAAG,EAAqC,CAAA;QAE1D,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YACvC,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,GAAG,GAAG,CAAC,MAAM,CAAA;YAC9B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,GAAG,CAAC,CAAA;YACzD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC,EAAE;YACF,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE;gBACtB,YAAY,CAAC,GAAG,CAAC,GAAG,IAAI,uBAAY,EAAE,CAAA;aACvC;YACD,YAAY,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;SACpD;QAED,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,aAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAzFjC,6BA0FC;AAzFe,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}
package/dist/VcfFeature/index.js CHANGED
@@ -34,7 +34,7 @@ class VCFFeature {
34
34
  const start = POS - 1;
35
35
  const [type, description] = (0, util_1.getSOTermAndDescription)(REF, ALT, this.parser);
36
36
  const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f === '<TRA>');
37
- const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.indexOf('<') !== -1);
37
+ const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
38
38
  return {
39
39
  refName: CHROM,
40
40
  start,
package/dist/VcfFeature/index.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/VcfFeature/util.js CHANGED
@@ -74,7 +74,7 @@ function getSOAndDescFromAltDefs(ref, alt, parser) {
74
74
  // try to look for a definition for a parent term if we can
75
75
  const modAlt = alt.split(':');
76
76
  if (modAlt.length > 1) {
77
- return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`, parser);
77
+ return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, -1).join(':')}>`, parser);
78
78
  }
79
79
  // no parent
80
80
  return [];
@@ -107,12 +107,9 @@ function getSOAndDescByExamination(ref, alt) {
107
107
  return ['sv', alt];
108
108
  }
109
109
  else if (ref.length === alt.length) {
110
- if (ref.split('').reverse().join('') === alt) {
111
- return ['inversion', makeDescriptionString('inversion', ref, alt)];
112
- }
113
- else {
114
- return ['substitution', makeDescriptionString('substitution', ref, alt)];
115
- }
110
+ return ref.split('').reverse().join('') === alt
111
+ ? ['inversion', makeDescriptionString('inversion', ref, alt)]
112
+ : ['substitution', makeDescriptionString('substitution', ref, alt)];
116
113
  }
117
114
  else if (ref.length <= alt.length) {
118
115
  return ['insertion', makeDescriptionString('insertion', ref, alt)];
package/dist/VcfFeature/util.js.map CHANGED
@@ -1 +1 @@
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package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts CHANGED
@@ -10,7 +10,7 @@ export default class extends BaseFeatureDataAdapter {
10
10
  vcf: TabixIndexedFile;
11
11
  parser: VcfParser;
12
12
  }>;
13
- getRefNames(opts?: BaseOptions): Promise<any>;
13
+ getRefNames(opts?: BaseOptions): Promise<string[]>;
14
14
  getHeader(): Promise<string>;
15
15
  getMetadata(): Promise<any>;
16
16
  getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
package/esm/ChordVariantDisplay/models/stateModelFactory.d.ts CHANGED
@@ -1,5 +1,6 @@
1
1
  /// <reference types="react" />
2
2
  import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
3
+ import { Feature } from '@jbrowse/core/util';
3
4
  /**
4
5
  * #stateModel ChordVariantDisplay
5
6
  * extends `BaseChordDisplay`
@@ -22,7 +23,9 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
22
23
  configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
23
24
  }, {
24
25
  rendererTypeName: string;
25
- error: unknown;
26
+ error: unknown; /**
27
+ * #property
28
+ */
26
29
  } & {
27
30
  readonly RenderingComponent: import("react").FC<{
28
31
  model: {
@@ -81,7 +84,7 @@ declare const stateModelFactory: (configSchema: AnyConfigurationSchemaType) => i
81
84
  renderingComponent: import("@jbrowse/core/util").AnyReactComponentType | undefined;
82
85
  refNameMap: Record<string, string> | undefined;
83
86
  } & {
84
- onChordClick(feature: import("@jbrowse/core/util").Feature): void;
87
+ onChordClick(feature: Feature): void;
85
88
  } & {
86
89
  readonly blockDefinitions: import("@jbrowse/plugin-circular-view/src/CircularView/models/slices").Slice[];
87
90
  renderProps(): any;
package/esm/ChordVariantDisplay/models/stateModelFactory.js CHANGED
@@ -39,7 +39,7 @@ const stateModelFactory = (configSchema) => {
39
39
  radius: view.radiusPx,
40
40
  blockDefinitions: self.blockDefinitions,
41
41
  config: self.configuration.renderer,
42
- onChordClick: self.onChordClick,
42
+ onChordClick: (arg) => self.onChordClick(arg),
43
43
  };
44
44
  },
45
45
  }));
package/esm/ChordVariantDisplay/models/stateModelFactory.js.map CHANGED
@@ -1 +1 @@
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1
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package/esm/LinearVariantDisplay/model.d.ts CHANGED
@@ -1,12 +1,13 @@
1
1
  /// <reference types="react" />
2
- import { Feature } from '@jbrowse/core/util/simpleFeature';
3
- import { LinearVariantDisplayConfigModel } from './configSchema';
2
+ import { Feature } from '@jbrowse/core/util';
3
+ import { Instance } from 'mobx-state-tree';
4
+ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
4
5
  /**
5
6
  * #stateModel LinearVariantDisplay
6
7
  * extends `LinearBasicDisplay`
7
8
  * very similar to basic display, but provides custom widget on feature click
8
9
  */
9
- export default function stateModelFactory(configSchema: LinearVariantDisplayConfigModel): import("mobx-state-tree").IModelType<{
10
+ export default function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
10
11
  id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
11
12
  type: import("mobx-state-tree").ISimpleType<string>;
12
13
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -63,7 +64,9 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
63
64
  } & {
64
65
  type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
65
66
  trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
66
- trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
67
+ trackShowDescriptions: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>; /**
68
+ * #action
69
+ */
67
70
  trackDisplayMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
68
71
  trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
69
72
  configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
@@ -134,10 +137,10 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
134
137
  message: string;
135
138
  featureIdUnderMouse: string | undefined;
136
139
  contextMenuFeature: Feature | undefined;
137
- estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
138
- estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
140
+ estimatedRegionsStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
141
+ estimatedRegionsStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
139
142
  } & {
140
- readonly height: any;
143
+ readonly height: number;
141
144
  readonly blockType: "dynamicBlocks" | "staticBlocks";
142
145
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
143
146
  } & {
@@ -148,7 +151,7 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
148
151
  } & {
149
152
  readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
150
153
  readonly featureUnderMouse: Feature | undefined;
151
- getFeatureOverlapping(blockKey: string, x: number, y: number): any;
154
+ getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
152
155
  getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
153
156
  searchFeatureByID(id: string): [number, number, number, number] | undefined;
154
157
  readonly currentBytesRequested: number;
@@ -158,19 +161,16 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
158
161
  readonly maxAllowableBytes: number;
159
162
  } & {
160
163
  setMessage(message: string): void;
164
+ } & {
161
165
  afterAttach(): void;
162
- estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
163
- headers?: Record<string, string> | undefined;
164
- signal?: AbortSignal | undefined;
165
- filters?: string[] | undefined;
166
- }): Promise<{}>;
167
- setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
168
- setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
169
- clearRegionStats(): void;
170
- setHeight(displayHeight: number): any;
166
+ estimateRegionsStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
167
+ setRegionsStatsP(arg: any): void;
168
+ setRegionsStats(estimatedRegionsStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
169
+ clearRegionsStats(): void;
170
+ setHeight(displayHeight: number): number;
171
171
  resizeHeight(distance: number): number;
172
172
  setScrollTop(scrollTop: number): void;
173
- updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
173
+ updateStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
174
174
  addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
175
175
  setCurrBpPerPx(n: number): void;
176
176
  deleteBlock(key: string): void;
@@ -184,18 +184,13 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
184
184
  readonly regionTooLargeReason: string;
185
185
  } & {
186
186
  reload(): Promise<void>;
187
+ } & {
187
188
  afterAttach(): void;
188
189
  } & {
189
190
  regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
190
191
  regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | null;
191
192
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
192
- contextMenuItems(): {
193
- label: string;
194
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
195
- muiName: string;
196
- };
197
- onClick: () => void;
198
- }[];
193
+ contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
199
194
  renderProps(): any;
200
195
  } & {
201
196
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
@@ -213,19 +208,19 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
213
208
  [x: string]: any;
214
209
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
215
210
  setSubschema(slotName: string, data: unknown): any;
216
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
211
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
217
212
  } & {
218
213
  toggleShowLabels(): void;
219
214
  toggleShowDescriptions(): void;
220
215
  setDisplayMode(val: string): void;
221
- setMaxHeight(val: number): void;
216
+ setMaxHeight(val?: number | undefined): void;
222
217
  } & {
223
218
  renderProps(): {
224
219
  config: {
225
220
  [x: string]: any;
226
221
  } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
227
222
  setSubschema(slotName: string, data: unknown): any;
228
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
223
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
229
224
  };
230
225
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
231
226
  } & {
@@ -234,3 +229,5 @@ export default function stateModelFactory(configSchema: LinearVariantDisplayConf
234
229
  */
235
230
  selectFeature(feature: Feature): Promise<void>;
236
231
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
232
+ export type LinearVariantDisplayStateModel = ReturnType<typeof stateModelFactory>;
233
+ export type LinearVariantDisplayModel = Instance<LinearVariantDisplayStateModel>;
package/esm/LinearVariantDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearVariantDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAA;AAC7E,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAA;AAC3D,OAAO,EACL,kBAAkB,EAClB,UAAU,EACV,iBAAiB,EACjB,yBAAyB,GAE1B,MAAM,oBAAoB,CAAA;AAE3B,OAAO,EAAE,8BAA8B,EAAE,MAAM,oCAAoC,CAAA;AACnF,OAAO,EAAY,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAGjD;;;;GAIG;AACH,MAAM,CAAC,OAAO,UAAU,iBAAiB,CACvC,YAAwC;IAExC,OAAO,KAAK;SACT,OAAO,CACN,sBAAsB,EACtB,8BAA8B,CAAC,YAAY,CAAC,EAC5C,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,sBAAsB,CAAC;QAC3C;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;KACpD,CAAC,CACH;SAEA,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,KAAK,CAAC,aAAa,CAAC,OAAgB;YAClC,MAAM,OAAO,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAChC,IAAI,yBAAyB,CAAC,OAAO,CAAC,EAAE;gBACtC,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAA;gBAC9B,MAAM,SAAS,GAAG,eAAe,CAAC,IAAI,CAAC,CAAA;gBACvC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,CAAA;gBACtC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAAC,CAAA;gBACpC,MAAM,aAAa,GAAG,OAAO,CAAC,KAAK,EAAE,SAAS,CAAC,CAAA;gBAC/C,MAAM,YAAY,GAAG,MAAM,UAAU,CAAC,IAAI,CACxC,SAAS,EACT,iBAAiB,EACjB;oBACE,aAAa;iBACd,CACF,CAAA;gBACD,OAAO,CAAC,UAAU,CAChB,OAAO,CAAC,SAAS,CAAC,sBAAsB,EAAE,gBAAgB,EAAE;oBAC1D,WAAW,EAAE,OAAO,CAAC,MAAM,EAAE;oBAC7B,IAAI;oBACJ,KAAK;oBACL,YAAY;iBACb,CAAC,CACH,CAAA;aACF;YAED,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;QAC/B,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
package/esm/VariantFeatureWidget/BreakendOptionDialog.js CHANGED
@@ -27,17 +27,18 @@ function BreakendOptionDialog({ model, handleClose, feature, viewType, }) {
27
27
  try {
28
28
  const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view);
29
29
  function remapIds(arr) {
30
- return arr.map((v) => ({
30
+ return arr.map(v => ({
31
31
  ...v,
32
- id: v.trackId + '-' + Math.random(),
32
+ id: `${v.trackId}-${Math.random()}`,
33
33
  }));
34
34
  }
35
35
  viewSnapshot.views[0].offsetPx -= view.width / 2 + 100;
36
36
  viewSnapshot.views[1].offsetPx -= view.width / 2 + 100;
37
37
  viewSnapshot.featureData = feature;
38
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
38
39
  const viewTracks = getSnapshot(view.tracks);
39
40
  viewSnapshot.views[0].tracks = remapIds(viewTracks);
40
- viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? viewTracks.slice().reverse() : viewTracks);
41
+ viewSnapshot.views[1].tracks = remapIds(mirrorTracks ? [...viewTracks].reverse() : viewTracks);
41
42
  session.addView('BreakpointSplitView', viewSnapshot);
42
43
  }
43
44
  catch (e) {
package/esm/VariantFeatureWidget/BreakendOptionDialog.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,aAAa,EACb,aAAa,EACb,gBAAgB,GACjB,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,UAAU;AACV,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAW,MAAM,oBAAoB,CAAA;AAExD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAA;AAEF,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,oBAAC,aAAa;YACZ,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBACD,SAAS,QAAQ,CAAC,GAAU;4BAC1B,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,CAAM,EAAE,EAAE,CAAC,CAAC;gCAC1B,GAAG,CAAC;gCACJ,EAAE,EAAE,CAAC,CAAC,OAAO,GAAG,GAAG,GAAG,IAAI,CAAC,MAAM,EAAE;6BACpC,CAAC,CAAC,CAAA;wBACL,CAAC;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,MAAM,UAAU,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAc,CAAA;wBACxD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;wBACnD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CACrC,YAAY,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,UAAU,CACzD,CAAA;wBAED,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,eAAe,QAAQ,CAAC,oBAAoB,CAAC,CAAA"}
1
+ {"version":3,"file":"BreakendOptionDialog.js","sourceRoot":"","sources":["../../src/VariantFeatureWidget/BreakendOptionDialog.tsx"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,aAAa,EACb,aAAa,EACb,gBAAgB,GACjB,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAA;AAC7C,UAAU;AACV,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,UAAU,EAAW,MAAM,oBAAoB,CAAA;AAExD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,KAAK,EAAE;QACL,OAAO,EAAE,OAAO;KACjB;CACF,CAAC,CAAA;AAEF,SAAS,oBAAoB,CAAC,EAC5B,KAAK,EACL,WAAW,EACX,OAAO,EACP,QAAQ,GAMT;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAClD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAEtD,OAAO,CACL,oBAAC,MAAM,IAAC,IAAI,QAAC,OAAO,EAAE,WAAW,EAAE,KAAK,EAAC,+BAA+B;QACtE,oBAAC,aAAa;YACZ,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,UAAU,EACnB,QAAQ,EAAE,GAAG,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC1C,EAEJ,KAAK,EAAC,+BAA+B,GACrC;YAEF,oBAAC,gBAAgB,IACf,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,OAAO,EACL,oBAAC,QAAQ,IACP,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,GAAG,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,GAC5C,EAEJ,KAAK,EAAC,qDAAqD,GAC3D,CACY;QAChB,oBAAC,aAAa;YACZ,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;oBACZ,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;oBACtB,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI;wBACF,MAAM,YAAY,GAAG,QAAQ,CAAC,2BAA2B,CACvD,OAAO,EACP,IAAI,CACL,CAAA;wBAMD,SAAS,QAAQ,CAAC,GAAY;4BAC5B,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;gCACnB,GAAG,CAAC;gCACJ,EAAE,EAAE,GAAG,CAAC,CAAC,OAAO,IAAI,IAAI,CAAC,MAAM,EAAE,EAAE;6BACpC,CAAC,CAAC,CAAA;wBACL,CAAC;wBACD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,GAAG,GAAG,CAAA;wBACtD,YAAY,CAAC,WAAW,GAAG,OAAO,CAAA;wBAClC,4EAA4E;wBAC5E,MAAM,UAAU,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAY,CAAA;wBACtD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAA;wBACnD,YAAY,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,GAAG,QAAQ,CACrC,YAAY,CAAC,CAAC,CAAC,CAAC,GAAG,UAAU,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,UAAU,CACtD,CAAA;wBAED,OAAO,CAAC,OAAO,CAAC,qBAAqB,EAAE,YAAY,CAAC,CAAA;qBACrD;oBAAC,OAAO,CAAC,EAAE;wBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;wBAChB,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;qBACvB;oBACD,WAAW,EAAE,CAAA;gBACf,CAAC,EACD,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,SAAS,eAGF;YACT,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE,CAAC,WAAW,EAAE,EAC5B,KAAK,EAAC,WAAW,EACjB,OAAO,EAAC,WAAW,aAGZ,CACK,CACT,CACV,CAAA;AACH,CAAC;AACD,eAAe,QAAQ,CAAC,oBAAoB,CAAC,CAAA"}
package/esm/VariantFeatureWidget/index.d.ts CHANGED
@@ -33,8 +33,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
33
33
  trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
34
34
  trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
35
35
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
36
- id: string;
37
36
  type: "BaseFeatureWidget";
37
+ id: string;
38
38
  track: import("mobx-state-tree").ReferenceIdentifier | undefined;
39
39
  view: import("mobx-state-tree").ReferenceIdentifier | undefined;
40
40
  trackId: string | undefined;
package/esm/VcfAdapter/VcfAdapter.d.ts CHANGED
@@ -11,7 +11,9 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
11
11
  getMetadata(): Promise<any>;
12
12
  setupP(): Promise<{
13
13
  header: string;
14
- intervalTree: Record<string, IntervalTree<any>>;
14
+ intervalTree: {
15
+ [key: string]: IntervalTree<any>;
16
+ };
15
17
  }>;
16
18
  setup(): Promise<{
17
19
  header: string;
package/esm/VcfAdapter/VcfAdapter.js CHANGED
@@ -46,22 +46,21 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
46
46
  }
47
47
  const str = new TextDecoder().decode(buffer);
48
48
  const { header, lines } = readVcf(str);
49
- const intervalTree = lines
50
- .map((line, id) => {
49
+ const intervalTree = {};
50
+ for (const obj of lines.map((line, id) => {
51
51
  var _a;
52
52
  const [refName, startP, , ref, , , , info] = line.split('\t');
53
53
  const start = +startP - 1;
54
- const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || start + ref.length);
54
+ const def = start + ref.length;
55
+ const end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || def);
55
56
  return { line, refName, start, end, id };
56
- })
57
- .reduce((acc, obj) => {
57
+ })) {
58
58
  const key = obj.refName;
59
- if (!acc[key]) {
60
- acc[key] = new IntervalTree();
59
+ if (!intervalTree[key]) {
60
+ intervalTree[key] = new IntervalTree();
61
61
  }
62
- acc[key].insert([obj.start, obj.end], obj);
63
- return acc;
64
- }, {});
62
+ intervalTree[key].insert([obj.start, obj.end], obj);
63
+ }
65
64
  return { header, intervalTree };
66
65
  }
67
66
  async setup() {
package/esm/VcfAdapter/VcfAdapter.js.map CHANGED
@@ -1 +1 @@
1
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+ {"version":3,"file":"VcfAdapter.js","sourceRoot":"","sources":["../../src/VcfAdapter/VcfAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,YAAY,MAAM,2BAA2B,CAAA;AACpD,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,GAAG,MAAM,WAAW,CAAA;AAE3B,QAAQ;AACR,OAAO,UAAU,MAAM,eAAe,CAAA;AAEtC,MAAM,OAAO,GAAG,CAAC,CAAS,EAAE,EAAE;IAC5B,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,MAAM,IAAI,GAAa,EAAE,CAAA;IACzB,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC;SAClB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;YACxB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAClB;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;SAChB;IACH,CAAC,CAAC,CAAA;IACJ,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;AACnD,CAAC,CAAA;AAED,SAAS,MAAM,CAAC,GAAW;IACzB,OAAO,GAAG,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,sBAAsB;IAQrD,KAAK,CAAC,SAAS;QACpB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACrC,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,CAAC,CAAA;QAC1C,OAAO,MAAM,CAAC,WAAW,EAAE,CAAA;IAC7B,CAAC;IAED,uCAAuC;IAChC,KAAK,CAAC,MAAM;QACjB,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,GAAG,GAAG,MAAM,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;QAE1E,MAAM,MAAM,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAEnD,2CAA2C;QAC3C,IAAI,MAAM,CAAC,MAAM,GAAG,SAAW,EAAE;YAC/B,MAAM,IAAI,KAAK,CAAC,4CAA4C,CAAC,CAAA;SAC9D;QAED,MAAM,GAAG,GAAG,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC5C,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAA;QACtC,MAAM,YAAY,GAAG,EAAqC,CAAA;QAE1D,KAAK,MAAM,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,EAAE,EAAE;;YACvC,MAAM,CAAC,OAAO,EAAE,MAAM,EAAE,AAAD,EAAG,GAAG,EAAE,AAAD,EAAG,AAAD,EAAG,AAAD,EAAG,IAAI,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC7D,MAAM,KAAK,GAAG,CAAC,MAAM,GAAG,CAAC,CAAA;YACzB,MAAM,GAAG,GAAG,KAAK,GAAG,GAAG,CAAC,MAAM,CAAA;YAC9B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAA,MAAA,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,0CAAG,CAAC,EAAE,IAAI,EAAE,KAAI,GAAG,CAAC,CAAA;YACzD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,EAAE,CAAA;QAC1C,CAAC,CAAC,EAAE;YACF,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAA;YACvB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,EAAE;gBACtB,YAAY,CAAC,GAAG,CAAC,GAAG,IAAI,YAAY,EAAE,CAAA;aACvC;YACD,YAAY,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;SACpD;QAED,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE;YACrB,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACzC,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;gBAC5B,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,WAAW,CAAA;IACzB,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,IAAiB,EAAE;QAC1C,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QAC3C,OAAO,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IAClC,CAAC;IAEM,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QACvD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;;YAChD,IAAI;gBACF,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;gBACtC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;gBACnD,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;gBAClC,MAAA,YAAY,CAAC,OAAO,CAAC,0CAAE,MAAM,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CACtD,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CAAC;oBACb,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;oBACjC,MAAM;oBACN,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,CAAC,CAAC,EAAE,EAAE;iBACzB,CAAC,CACH,CACF,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;aACpB;YAAC,OAAO,CAAC,EAAE;gBACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;aAClB;QACH,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEM,aAAa,KAAU,CAAC;;AAxFjB,uBAAY,GAAG,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA"}
package/esm/VcfFeature/index.js CHANGED
@@ -32,7 +32,7 @@ export default class VCFFeature {
32
32
  const start = POS - 1;
33
33
  const [type, description] = getSOTermAndDescription(REF, ALT, this.parser);
34
34
  const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f === '<TRA>');
35
- const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.indexOf('<') !== -1);
35
+ const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
36
36
  return {
37
37
  refName: CHROM,
38
38
  start,
package/esm/VcfFeature/index.js.map CHANGED
@@ -1 +1 @@
1
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package/esm/VcfFeature/util.js CHANGED
@@ -70,7 +70,7 @@ export function getSOAndDescFromAltDefs(ref, alt, parser) {
70
70
  // try to look for a definition for a parent term if we can
71
71
  const modAlt = alt.split(':');
72
72
  if (modAlt.length > 1) {
73
- return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`, parser);
73
+ return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, -1).join(':')}>`, parser);
74
74
  }
75
75
  // no parent
76
76
  return [];
@@ -102,12 +102,9 @@ export function getSOAndDescByExamination(ref, alt) {
102
102
  return ['sv', alt];
103
103
  }
104
104
  else if (ref.length === alt.length) {
105
- if (ref.split('').reverse().join('') === alt) {
106
- return ['inversion', makeDescriptionString('inversion', ref, alt)];
107
- }
108
- else {
109
- return ['substitution', makeDescriptionString('substitution', ref, alt)];
110
- }
105
+ return ref.split('').reverse().join('') === alt
106
+ ? ['inversion', makeDescriptionString('inversion', ref, alt)]
107
+ : ['substitution', makeDescriptionString('substitution', ref, alt)];
111
108
  }
112
109
  else if (ref.length <= alt.length) {
113
110
  return ['insertion', makeDescriptionString('insertion', ref, alt)];
package/esm/VcfFeature/util.js.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/VcfFeature/util.ts"],"names":[],"mappings":"AAAA,OAAY,EAAE,aAAa,EAAE,MAAM,WAAW,CAAA;AAE9C,MAAM,WAAW,GAA0C;IACzD,GAAG,EAAE,UAAU;IACf,GAAG,EAAE,WAAW;IAChB,GAAG,EAAE,aAAa;IAClB,GAAG,EAAE,WAAW;IAChB,MAAM,EAAE,sBAAsB;IAC9B,GAAG,EAAE,uBAAuB;IAC5B,GAAG,EAAE,eAAe;IACpB,YAAY,EAAE,oBAAoB;IAClC,OAAO,EAAE,kBAAkB;IAC3B,GAAG,EAAE,kBAAkB;CACxB,CAAA;AAED;;GAEG;AACH,MAAM,UAAU,uBAAuB,CACrC,GAAW,EACX,GAAa,EACb,MAAW;IAEX,uDAAuD;IACvD,IAAI,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;QAC5B,OAAO,CAAC,QAAQ,EAAE,wBAAwB,CAAC,CAAA;KAC5C;IAED,MAAM,OAAO,GAAG,IAAI,GAAG,EAAU,CAAA;IACjC,IAAI,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;IACpC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACd,IAAI,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,uBAAuB,CAAC,GAAG,EAAE,CAAC,EAAE,MAAM,CAAC,CAAA;QACnE,IAAI,CAAC,MAAM,EAAE;YACX,CAAC;YAAA,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,yBAAyB,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;SAC3D;QACD,IAAI,MAAM,IAAI,WAAW,EAAE;YACzB,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACnB,YAAY,CAAC,GAAG,CAAC,WAAW,CAAC,CAAA;SAC9B;IACH,CAAC,CAAC,CAAA;IAEF,6EAA6E;IAC7E,IAAI,YAAY,CAAC,IAAI,GAAG,CAAC,EAAE;QACzB,MAAM,KAAK,GAAG,CAAC,GAAG,YAAY,CAAC,CAAA;QAC/B,MAAM,QAAQ,GAAG,IAAI,GAAG,CACtB,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YACf,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QACrC,CAAC,CAAC,CACH,CAAA;QAED,YAAY,GAAG,IAAI,GAAG,CACpB,CAAC,GAAG,QAAQ,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;YACzB,MAAM,QAAQ,GAAG,KAAK;iBACnB,GAAG,CAAC,IAAI,CAAC,EAAE;gBACV,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBAC9B,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;YACrD,CAAC,CAAC;iBACD,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAEnB,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,GAAG,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;QACvE,CAAC,CAAC,CACH,CAAA;KACF;IACD,IAAI,OAAO,CAAC,IAAI,EAAE;QAChB,OAAO,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;KAC7D;IACD,OAAO,EAAE,CAAA;AACX,CAAC;AAED,MAAM,UAAU,uBAAuB,CACrC,GAAW,EACX,GAAW,EACX,MAAW;IAEX,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE;QACnD,OAAO,EAAE,CAAA;KACV;IAED,iDAAiD;IACjD,IAAI,MAAM,GAAG,WAAW,CAAC,GAAG,CAAC,CAAA;IAC7B,gEAAgE;IAChE,IAAI,CAAC,MAAM,IAAI,MAAM,CAAC,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE;QAC7C,MAAM,GAAG,kBAAkB,CAAA;KAC5B;IACD,IAAI,MAAM,EAAE;QACV,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAA;KACrB;IAED,2DAA2D;IAC3D,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC7B,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE;QACrB,OAAO,uBAAuB,CAC5B,GAAG,EACH,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EACpC,MAAM,CACP,CAAA;KACF;IAED,YAAY;IACZ,OAAO,EAAE,CAAA;AACX,CAAC;AAED,0EAA0E;AAC1E,yEAAyE;AACzE,OAAO;AACP,MAAM,UAAU,yBAAyB,CAAC,GAAW,EAAE,GAAW;IAChE,MAAM,GAAG,GAAG,aAAa,CAAC,GAAG,CAAC,CAAA;IAC9B,IAAI,GAAG,EAAE;QACP,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;KACzB;SAAM,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE;QAC/C,OAAO,CAAC,KAAK,EAAE,qBAAqB,CAAC,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACvD;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAA;KAC1B;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;KACzB;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC,CAAA;KACzB;SAAM,IAAI,GAAG,KAAK,OAAO,EAAE;QAC1B,OAAO,CAAC,eAAe,EAAE,GAAG,CAAC,CAAA;KAC9B;SAAM,IAAI,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE;QAC5B,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;KACnB;SAAM,IAAI,GAAG,CAAC,MAAM,KAAK,GAAG,CAAC,MAAM,EAAE;QACpC,OAAO,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,GAAG;YAC7C,CAAC,CAAC,CAAC,WAAW,EAAE,qBAAqB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC;YAC7D,CAAC,CAAC,CAAC,cAAc,EAAE,qBAAqB,CAAC,cAAc,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACtE;SAAM,IAAI,GAAG,CAAC,MAAM,IAAI,GAAG,CAAC,MAAM,EAAE;QACnC,OAAO,CAAC,WAAW,EAAE,qBAAqB,CAAC,WAAW,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACnE;SAAM,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE;QAClC,OAAO,CAAC,UAAU,EAAE,qBAAqB,CAAC,UAAU,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;KACjE;IAED,OAAO,CAAC,OAAO,EAAE,qBAAqB,CAAC,OAAO,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;AAC5D,CAAC;AAED,SAAS,qBAAqB,CAAC,MAAc,EAAE,GAAW,EAAE,GAAW;IACrE,OAAO,GAAG,MAAM,IAAI,GAAG,OAAO,GAAG,EAAE,CAAA;AACrC,CAAC"}
package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts CHANGED
@@ -10,7 +10,7 @@ export default class extends BaseFeatureDataAdapter {
10
10
  vcf: TabixIndexedFile;
11
11
  parser: VcfParser;
12
12
  }>;
13
- getRefNames(opts?: BaseOptions): Promise<any>;
13
+ getRefNames(opts?: BaseOptions): Promise<string[]>;
14
14
  getHeader(): Promise<string>;
15
15
  getMetadata(): Promise<any>;
16
16
  getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-variants",
3
- "version": "2.4.0",
3
+ "version": "2.4.2",
4
4
  "description": "JBrowse 2 variant adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -39,7 +39,7 @@
39
39
  "dependencies": {
40
40
  "@flatten-js/interval-tree": "^1.0.15",
41
41
  "@gmod/bgzf-filehandle": "^1.4.3",
42
- "@gmod/tabix": "^1.5.2",
42
+ "@gmod/tabix": "^1.5.6",
43
43
  "@gmod/vcf": "^5.0.9",
44
44
  "@mui/icons-material": "^5.0.2",
45
45
  "@mui/x-data-grid": "^5.0.1",
@@ -64,5 +64,5 @@
64
64
  "distModule": "esm/index.js",
65
65
  "srcModule": "src/index.ts",
66
66
  "module": "esm/index.js",
67
- "gitHead": "78707a2bc3ba8489f26a590ef83f62ede945d048"
67
+ "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
68
68
  }
package/src/ChordVariantDisplay/models/stateModelFactory.ts CHANGED
@@ -4,7 +4,7 @@ import {
4
4
  ConfigurationReference,
5
5
  } from '@jbrowse/core/configuration'
6
6
  import { types } from 'mobx-state-tree'
7
- import { getContainingView } from '@jbrowse/core/util'
7
+ import { Feature, getContainingView } from '@jbrowse/core/util'
8
8
  import { getParentRenderProps } from '@jbrowse/core/util/tracks'
9
9
 
10
10
  /**
@@ -48,7 +48,7 @@ const stateModelFactory = (configSchema: AnyConfigurationSchemaType) => {
48
48
  radius: view.radiusPx,
49
49
  blockDefinitions: self.blockDefinitions,
50
50
  config: self.configuration.renderer,
51
- onChordClick: self.onChordClick,
51
+ onChordClick: (arg: Feature) => self.onChordClick(arg),
52
52
  }
53
53
  },
54
54
  }))
package/src/LinearVariantDisplay/model.ts CHANGED
@@ -5,12 +5,12 @@ import {
5
5
  getSession,
6
6
  getContainingView,
7
7
  isSessionModelWithWidgets,
8
+ Feature,
8
9
  } from '@jbrowse/core/util'
9
10
 
10
- import { Feature } from '@jbrowse/core/util/simpleFeature'
11
11
  import { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view'
12
- import { types } from 'mobx-state-tree'
13
- import { LinearVariantDisplayConfigModel } from './configSchema'
12
+ import { Instance, types } from 'mobx-state-tree'
13
+ import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
14
14
 
15
15
  /**
16
16
  * #stateModel LinearVariantDisplay
@@ -18,7 +18,7 @@ import { LinearVariantDisplayConfigModel } from './configSchema'
18
18
  * very similar to basic display, but provides custom widget on feature click
19
19
  */
20
20
  export default function stateModelFactory(
21
- configSchema: LinearVariantDisplayConfigModel,
21
+ configSchema: AnyConfigurationSchemaType,
22
22
  ) {
23
23
  return types
24
24
  .compose(
@@ -35,6 +35,7 @@ export default function stateModelFactory(
35
35
  configuration: ConfigurationReference(configSchema),
36
36
  }),
37
37
  )
38
+
38
39
  .actions(self => ({
39
40
  /**
40
41
  * #action
@@ -68,3 +69,8 @@ export default function stateModelFactory(
68
69
  },
69
70
  }))
70
71
  }
72
+
73
+ export type LinearVariantDisplayStateModel = ReturnType<
74
+ typeof stateModelFactory
75
+ >
76
+ export type LinearVariantDisplayModel = Instance<LinearVariantDisplayStateModel>
package/src/VariantFeatureWidget/BreakendOptionDialog.tsx CHANGED
@@ -70,19 +70,25 @@ function BreakendOptionDialog({
70
70
  feature,
71
71
  view,
72
72
  )
73
- function remapIds(arr: any[]) {
74
- return arr.map((v: any) => ({
73
+
74
+ interface Track {
75
+ trackId: string
76
+ [key: string]: unknown
77
+ }
78
+ function remapIds(arr: Track[]) {
79
+ return arr.map(v => ({
75
80
  ...v,
76
- id: v.trackId + '-' + Math.random(),
81
+ id: `${v.trackId}-${Math.random()}`,
77
82
  }))
78
83
  }
79
84
  viewSnapshot.views[0].offsetPx -= view.width / 2 + 100
80
85
  viewSnapshot.views[1].offsetPx -= view.width / 2 + 100
81
86
  viewSnapshot.featureData = feature
82
- const viewTracks = getSnapshot(view.tracks) as unknown[]
87
+ // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
88
+ const viewTracks = getSnapshot(view.tracks) as Track[]
83
89
  viewSnapshot.views[0].tracks = remapIds(viewTracks)
84
90
  viewSnapshot.views[1].tracks = remapIds(
85
- mirrorTracks ? viewTracks.slice().reverse() : viewTracks,
91
+ mirrorTracks ? [...viewTracks].reverse() : viewTracks,
86
92
  )
87
93
 
88
94
  session.addView('BreakpointSplitView', viewSnapshot)
package/src/VariantFeatureWidget/VariantFeatureWidget.test.tsx CHANGED
@@ -18,7 +18,7 @@ test('renders with just the required model elements', () => {
18
18
  const model = Session.create(
19
19
  {
20
20
  widget: {
21
- // @ts-ignore
21
+ // @ts-expect-error
22
22
  type: 'VariantFeatureWidget',
23
23
  },
24
24
  },
package/src/VcfAdapter/VcfAdapter.ts CHANGED
@@ -65,22 +65,21 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
65
65
 
66
66
  const str = new TextDecoder().decode(buffer)
67
67
  const { header, lines } = readVcf(str)
68
-
69
- const intervalTree = lines
70
- .map((line, id) => {
71
- const [refName, startP, , ref, , , , info] = line.split('\t')
72
- const start = +startP - 1
73
- const end = +(info.match(/END=(\d+)/)?.[1].trim() || start + ref.length)
74
- return { line, refName, start, end, id }
75
- })
76
- .reduce((acc, obj) => {
77
- const key = obj.refName
78
- if (!acc[key]) {
79
- acc[key] = new IntervalTree()
80
- }
81
- acc[key].insert([obj.start, obj.end], obj)
82
- return acc
83
- }, {} as Record<string, IntervalTree>)
68
+ const intervalTree = {} as { [key: string]: IntervalTree }
69
+
70
+ for (const obj of lines.map((line, id) => {
71
+ const [refName, startP, , ref, , , , info] = line.split('\t')
72
+ const start = +startP - 1
73
+ const def = start + ref.length
74
+ const end = +(info.match(/END=(\d+)/)?.[1].trim() || def)
75
+ return { line, refName, start, end, id }
76
+ })) {
77
+ const key = obj.refName
78
+ if (!intervalTree[key]) {
79
+ intervalTree[key] = new IntervalTree()
80
+ }
81
+ intervalTree[key].insert([obj.start, obj.end], obj)
82
+ }
84
83
 
85
84
  return { header, intervalTree }
86
85
  }
package/src/VcfFeature/index.ts CHANGED
@@ -79,7 +79,7 @@ export default class VCFFeature implements Feature {
79
79
  const start = POS - 1
80
80
  const [type, description] = getSOTermAndDescription(REF, ALT, this.parser)
81
81
  const isTRA = ALT?.some(f => f === '<TRA>')
82
- const isSymbolic = ALT?.some(f => f.indexOf('<') !== -1)
82
+ const isSymbolic = ALT?.some(f => f.includes('<'))
83
83
 
84
84
  return {
85
85
  refName: CHROM,
package/src/VcfFeature/util.ts CHANGED
@@ -92,7 +92,7 @@ export function getSOAndDescFromAltDefs(
92
92
  if (modAlt.length > 1) {
93
93
  return getSOAndDescFromAltDefs(
94
94
  ref,
95
- `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`,
95
+ `<${modAlt.slice(0, -1).join(':')}>`,
96
96
  parser,
97
97
  )
98
98
  }
@@ -121,11 +121,9 @@ export function getSOAndDescByExamination(ref: string, alt: string) {
121
121
  } else if (alt.includes('<')) {
122
122
  return ['sv', alt]
123
123
  } else if (ref.length === alt.length) {
124
- if (ref.split('').reverse().join('') === alt) {
125
- return ['inversion', makeDescriptionString('inversion', ref, alt)]
126
- } else {
127
- return ['substitution', makeDescriptionString('substitution', ref, alt)]
128
- }
124
+ return ref.split('').reverse().join('') === alt
125
+ ? ['inversion', makeDescriptionString('inversion', ref, alt)]
126
+ : ['substitution', makeDescriptionString('substitution', ref, alt)]
129
127
  } else if (ref.length <= alt.length) {
130
128
  return ['insertion', makeDescriptionString('insertion', ref, alt)]
131
129
  } else if (ref.length > alt.length) {
package/src/VcfTabixAdapter/__snapshots__/VcfTabixAdapter.test.ts.snap CHANGED
@@ -66,7 +66,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
66
66
  },
67
67
  "start": 276,
68
68
  "type": "SNV",
69
- "uniqueId": "test-vcf-604452",
69
+ "uniqueId": "test-vcf-604453",
70
70
  },
71
71
  {
72
72
  "ALT": [
@@ -132,7 +132,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
132
132
  },
133
133
  "start": 1693,
134
134
  "type": "SNV",
135
- "uniqueId": "test-vcf-604550",
135
+ "uniqueId": "test-vcf-604551",
136
136
  },
137
137
  {
138
138
  "ALT": [
@@ -198,7 +198,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
198
198
  },
199
199
  "start": 2643,
200
200
  "type": "SNV",
201
- "uniqueId": "test-vcf-604667",
201
+ "uniqueId": "test-vcf-604668",
202
202
  },
203
203
  {
204
204
  "ALT": [
@@ -258,7 +258,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
258
258
  },
259
259
  "start": 3212,
260
260
  "type": "SNV",
261
- "uniqueId": "test-vcf-604784",
261
+ "uniqueId": "test-vcf-604785",
262
262
  },
263
263
  {
264
264
  "ALT": [
@@ -319,7 +319,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
319
319
  },
320
320
  "start": 3857,
321
321
  "type": "deletion",
322
- "uniqueId": "test-vcf-604886",
322
+ "uniqueId": "test-vcf-604887",
323
323
  },
324
324
  ]
325
325
  `;