@jbrowse/plugin-variants 4.1.14 → 4.1.15

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Files changed (16) hide show
  1. package/esm/LDDisplay/SharedLDConfigSchema.d.ts +1 -1
  2. package/esm/LDDisplay/configSchema1.d.ts +1 -1
  3. package/esm/LDDisplay/configSchema2.d.ts +1 -1
  4. package/esm/LinearVariantDisplay/model.d.ts +1 -0
  5. package/esm/MultiLinearVariantDisplay/configSchema.d.ts +2 -2
  6. package/esm/MultiLinearVariantDisplay/model.d.ts +3 -0
  7. package/esm/MultiLinearVariantMatrixDisplay/configSchema.d.ts +1 -1
  8. package/esm/MultiLinearVariantMatrixDisplay/model.d.ts +3 -0
  9. package/esm/PlinkLDAdapter/configSchemaTabix.d.ts +1 -1
  10. package/esm/VariantFeatureWidget/stateModelFactory.d.ts +5 -5
  11. package/esm/VariantRPC/executeClusterGenotypeMatrix.js +7 -7
  12. package/esm/VcfTabixAdapter/configSchema.d.ts +1 -1
  13. package/esm/shared/MultiVariantBaseModel.d.ts +3 -0
  14. package/esm/shared/SharedVariantConfigSchema.d.ts +1 -1
  15. package/esm/shared/components/MultiVariantTooltip.d.ts +2 -2
  16. package/package.json +11 -11
package/esm/LDDisplay/SharedLDConfigSchema.d.ts CHANGED
@@ -13,7 +13,7 @@ export default function sharedLDConfigFactory(): import("@jbrowse/core/configura
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  };
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  ldMetric: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"r2" | "dprime">;
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  defaultValue: string;
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  };
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  colorScheme: {
package/esm/LDDisplay/configSchema1.d.ts CHANGED
@@ -26,7 +26,7 @@ export default function configSchemaF(_pluginManager: PluginManager): import("@j
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  };
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  ldMetric: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"r2" | "dprime">;
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  defaultValue: string;
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  };
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  colorScheme: {
package/esm/LDDisplay/configSchema2.d.ts CHANGED
@@ -26,7 +26,7 @@ export default function configSchemaF(_pluginManager: PluginManager): import("@j
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  };
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  ldMetric: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"r2" | "dprime">;
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  defaultValue: string;
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  };
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  colorScheme: {
package/esm/LinearVariantDisplay/model.d.ts CHANGED
@@ -1093,6 +1093,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
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  };
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  renderProps(): any;
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  } & {
package/esm/MultiLinearVariantDisplay/configSchema.d.ts CHANGED
@@ -2,7 +2,7 @@ import type PluginManager from '@jbrowse/core/PluginManager';
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  export default function VariantConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  defaultRendering: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"multivariant">;
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  defaultValue: string;
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  };
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  renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
@@ -27,7 +27,7 @@ export default function VariantConfigFactory(pluginManager: PluginManager): impo
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  };
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  renderingMode: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"alleleCount" | "phased">;
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  defaultValue: string;
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  };
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  minorAlleleFrequencyFilter: {
package/esm/MultiLinearVariantDisplay/model.d.ts CHANGED
@@ -1103,6 +1103,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
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  };
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  renderProps(): any;
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  } & {
@@ -2445,6 +2446,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
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  };
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  renderProps(): any;
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  } & {
@@ -3733,6 +3735,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
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  };
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  renderProps(): any;
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  } & {
package/esm/MultiLinearVariantMatrixDisplay/configSchema.d.ts CHANGED
@@ -19,7 +19,7 @@ export default function configSchemaF(pluginManager: PluginManager): import("@jb
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  };
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  renderingMode: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"alleleCount" | "phased">;
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  defaultValue: string;
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  };
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  minorAlleleFrequencyFilter: {
package/esm/MultiLinearVariantMatrixDisplay/model.d.ts CHANGED
@@ -1104,6 +1104,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
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  };
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  renderProps(): any;
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  } & {
@@ -2446,6 +2447,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
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  };
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  renderProps(): any;
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  } & {
@@ -3734,6 +3736,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
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  };
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  renderProps(): any;
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  } & {
package/esm/PlinkLDAdapter/configSchemaTabix.d.ts CHANGED
@@ -8,7 +8,7 @@ declare const PlinkLDTabixAdapter: import("@jbrowse/core/configuration/configura
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  };
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  index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  indexType: {
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"TBI" | "CSI">;
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  type: string;
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  defaultValue: string;
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  };
package/esm/VariantFeatureWidget/stateModelFactory.d.ts CHANGED
@@ -3,9 +3,9 @@ import type { Instance } from '@jbrowse/mobx-state-tree';
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  export declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("@jbrowse/mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
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- featureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
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+ featureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
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  formattedFields: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
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- unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
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+ unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
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  view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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  track: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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  trackId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -54,9 +54,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  } & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
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  id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
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  type: import("@jbrowse/mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
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- featureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
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+ featureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
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  formattedFields: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
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- unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
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+ unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget").MaybeSerializedFeat>;
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  view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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  track: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
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  trackId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -94,10 +94,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
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  type: "BaseFeatureWidget";
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  trackId: string | undefined;
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  sequenceFeatureDetails: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{}>;
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- descriptions: Record<string, unknown> | undefined;
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  formattedFields: any;
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  trackType: string | undefined;
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  maxDepth: number | undefined;
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+ descriptions: Record<string, unknown> | undefined;
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  finalizedFeatureData: any;
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  } & import("@jbrowse/mobx-state-tree")._NotCustomized>;
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  export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
package/esm/VariantRPC/executeClusterGenotypeMatrix.js CHANGED
@@ -1,5 +1,5 @@
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- import { clusterData, toNewick } from '@gmod/hclust';
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- import { createStopTokenChecker } from '@jbrowse/core/util/stopToken';
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+ import { clusterObject, toNewick } from '@gmod/hclust';
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+ import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
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  import { getGenotypeMatrix } from "./getGenotypeMatrix.js";
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  import { getPhasedGenotypeMatrix } from "./getPhasedGenotypeMatrix.js";
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  export async function executeClusterGenotypeMatrix({ pluginManager, args, }) {
@@ -12,12 +12,12 @@ export async function executeClusterGenotypeMatrix({ pluginManager, args, }) {
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  args: { ...argsWithCheck, sampleInfo },
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  })
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  : await getGenotypeMatrix({ pluginManager, args: argsWithCheck });
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- const sampleLabels = Object.keys(matrix);
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- const result = await clusterData({
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- data: Object.values(matrix),
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- sampleLabels,
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- stopToken: args.stopToken,
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+ const result = await clusterObject({
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+ data: matrix,
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  onProgress: args.statusCallback,
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+ checkCancellation: () => {
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+ checkStopToken2(stopTokenCheck);
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+ },
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  });
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  return {
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  order: result.order,
package/esm/VcfTabixAdapter/configSchema.d.ts CHANGED
@@ -8,7 +8,7 @@ declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configuration
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  };
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  index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
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  indexType: {
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"TBI" | "CSI">;
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  type: string;
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  defaultValue: string;
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  };
package/esm/shared/MultiVariantBaseModel.d.ts CHANGED
@@ -1105,6 +1105,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
1105
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  onMouseMove(_: unknown, featureId?: string): void;
1106
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  onMouseLeave(_: unknown): void;
1107
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
1108
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  };
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  renderProps(): any;
1110
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  } & {
@@ -2447,6 +2448,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
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  };
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  renderProps(): any;
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  } & {
@@ -3735,6 +3737,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
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  onMouseMove(_: unknown, featureId?: string): void;
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  onMouseLeave(_: unknown): void;
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  onContextMenu(_: unknown): void;
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+ onFeatureClick(_: unknown, featureId?: string): void;
3738
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  };
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  renderProps(): any;
3740
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  } & {
package/esm/shared/SharedVariantConfigSchema.d.ts CHANGED
@@ -13,7 +13,7 @@ export default function sharedVariantConfigFactory(): import("@jbrowse/core/conf
13
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  };
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  renderingMode: {
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  type: string;
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- model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
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+ model: import("@jbrowse/mobx-state-tree").ISimpleType<"alleleCount" | "phased">;
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  defaultValue: string;
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  };
19
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  minorAlleleFrequencyFilter: {
package/esm/shared/components/MultiVariantTooltip.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- declare const MultiVariantTooltip: import("react").NamedExoticComponent<{
1
+ declare const MultiVariantTooltip: import("react").MemoExoticComponent<({ source, x, y, }: {
2
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  source: {
3
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  color?: string;
4
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  name?: string;
@@ -6,5 +6,5 @@ declare const MultiVariantTooltip: import("react").NamedExoticComponent<{
6
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  };
7
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  x: number;
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  y: number;
9
- }>;
9
+ }) => import("react/jsx-runtime").JSX.Element>;
10
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  export default MultiVariantTooltip;
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
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  "name": "@jbrowse/plugin-variants",
3
- "version": "4.1.14",
3
+ "version": "4.1.15",
4
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  "type": "module",
5
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  "description": "JBrowse 2 variant adapters, tracks, etc.",
6
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  "keywords": [
@@ -22,14 +22,14 @@
22
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  ],
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  "dependencies": {
24
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  "@flatten-js/interval-tree": "^2.0.3",
25
- "@gmod/hclust": "^1.0.7",
26
- "@gmod/tabix": "^3.2.2",
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+ "@gmod/hclust": "^3.0.4",
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+ "@gmod/tabix": "^3.3.1",
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  "@gmod/vcf": "^7.0.0",
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- "@jbrowse/mobx-state-tree": "^5.5.0",
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- "@mui/icons-material": "^7.3.8",
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- "@mui/material": "^7.3.8",
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+ "@jbrowse/mobx-state-tree": "^5.6.0",
29
+ "@mui/icons-material": "^7.3.9",
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+ "@mui/material": "^7.3.9",
31
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  "@mui/x-charts-vendor": "^8.26.0",
32
- "@mui/x-data-grid": "^8.27.3",
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+ "@mui/x-data-grid": "^8.28.2",
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  "@types/file-saver-es": "^2.0.3",
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  "copy-to-clipboard": "^3.3.3",
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  "escape-html": "^1.0.3",
@@ -38,10 +38,10 @@
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  "mobx": "^6.15.0",
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  "mobx-react": "^9.2.1",
40
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  "rxjs": "^7.8.2",
41
- "@jbrowse/plugin-circular-view": "^4.1.14",
42
- "@jbrowse/core": "^4.1.14",
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- "@jbrowse/plugin-linear-genome-view": "^4.1.14",
44
- "@jbrowse/sv-core": "^4.1.14"
41
+ "@jbrowse/plugin-circular-view": "^4.1.15",
42
+ "@jbrowse/sv-core": "^4.1.15",
43
+ "@jbrowse/plugin-linear-genome-view": "^4.1.15",
44
+ "@jbrowse/core": "^4.1.15"
45
45
  },
46
46
  "peerDependencies": {
47
47
  "react": ">=18.0.0"