@jbrowse/plugin-variants 2.10.3 → 2.11.1

package/dist/ChordVariantDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ChordVariantDisplayF(pluginManager: PluginManager): void;

package/dist/ChordVariantDisplay/index.js

@@ -8,7 +8,7 @@ const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 // locals
 const configSchema_1 = __importDefault(require("./models/configSchema"));
 const stateModelFactory_1 = __importDefault(require("./models/stateModelFactory"));
-exports.default = (pluginManager) => {
+function ChordVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         const stateModel = (0, stateModelFactory_1.default)(configSchema);
@@ -22,4 +22,5 @@ exports.default = (pluginManager) => {
             ReactComponent: plugin_circular_view_1.BaseChordDisplayComponent,
         });
     });
-};
+}
+exports.default = ChordVariantDisplayF;

package/dist/LinearVariantDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearVariantDisplayF(pluginManager: PluginManager): void;

package/dist/LinearVariantDisplay/index.js

@@ -7,7 +7,7 @@ const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view"
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 const model_1 = __importDefault(require("./model"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function LinearVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
@@ -20,4 +20,5 @@ exports.default = (pluginManager) => {
             ReactComponent: plugin_linear_genome_view_1.BaseLinearDisplayComponent,
         });
     });
-};
+}
+exports.default = LinearVariantDisplayF;

package/dist/StructuralVariantChordRenderer/Chord.js

@@ -87,7 +87,7 @@ const Chord = (0, mobx_react_1.observer)(function Chord({ feature, blocksForRefs
         const hoverStrokeColor = (0, configuration_1.readConfObject)(config, 'strokeColorHover', {
             feature,
         });
-        return (react_1.default.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), stroke: hovered ? hoverStrokeColor : strokeColor, strokeWidth: hovered ? 3 : 1, onClick: evt => {
+        return (react_1.default.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), ...(0, util_1.getStrokeProps)(hovered ? hoverStrokeColor : strokeColor), strokeWidth: hovered ? 3 : 1, onClick: evt => {
                 if (endBlock && startBlock) {
                     onClick(feature, startBlock.region, endBlock.region, evt);
                 }

package/dist/StructuralVariantChordRenderer/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function StructuralVariantChordRendererF(pluginManager: PluginManager): void;

package/dist/StructuralVariantChordRenderer/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const CircularChordRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 const ReactComponent_1 = __importDefault(require("./ReactComponent"));
-exports.default = (pluginManager) => {
+function StructuralVariantChordRendererF(pluginManager) {
     pluginManager.addRendererType(() => new CircularChordRendererType_1.default({
         name: 'StructuralVariantChordRenderer',
         displayName: 'SV chord renderer',
@@ -14,4 +14,5 @@ exports.default = (pluginManager) => {
         configSchema: configSchema_1.default,
         pluginManager,
     }));
-};
+}
+exports.default = StructuralVariantChordRendererF;

package/dist/VariantFeatureWidget/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VariantFeatureWidgetF(pluginManager: PluginManager): void;

package/dist/VariantFeatureWidget/index.js

@@ -30,7 +30,7 @@ const react_1 = require("react");
 const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
 const stateModelFactory_1 = require("./stateModelFactory");
 const configSchema_1 = require("./configSchema");
-exports.default = (pluginManager) => {
+function VariantFeatureWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType_1.default({
         name: 'VariantFeatureWidget',
         heading: 'Feature details',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
         stateModel: (0, stateModelFactory_1.stateModelFactory)(pluginManager),
         ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./VariantFeatureWidget')))),
     }));
-};
+}
+exports.default = VariantFeatureWidgetF;

package/dist/VariantFeatureWidget/stateModelFactory.d.ts

@@ -11,6 +11,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
@@ -37,6 +48,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
@@ -46,6 +68,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/dist/VariantTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function VariantTrackF(pm: PluginManager): void;

package/dist/VariantTrack/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pm) => {
+function VariantTrackF(pm) {
     pm.addTrackType(() => {
         const configSchema = (0, configSchema_1.default)(pm);
         return new TrackType_1.default({
@@ -16,4 +16,5 @@ exports.default = (pm) => {
             stateModel: (0, models_1.createBaseTrackModel)(pm, 'VariantTrack', configSchema),
         });
     });
-};
+}
+exports.default = VariantTrackF;

package/dist/VcfAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VcfAdapterF(pluginManager: PluginManager): void;

package/dist/VcfAdapter/index.js

@@ -28,11 +28,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function VcfAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'VcfAdapter',
         displayName: 'VCF adapter',
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = VcfAdapterF;

package/dist/VcfFeature/util.d.ts

@@ -3,5 +3,5 @@ import VCF from '@gmod/vcf';
  * Get a sequence ontology (SO) term that describes the variant type
  */
 export declare function getSOTermAndDescription(ref: string, alt: string[], parser: VCF): string[];
-export declare function getSOAndDescFromAltDefs(ref: string, alt: string, parser: VCF): string[];
+export declare function getSOAndDescFromAltDefs(alt: string, parser: VCF): string[];
 export declare function getSOAndDescByExamination(ref: string, alt: string): string[];

package/dist/VcfFeature/util.js

@@ -25,7 +25,7 @@ function getSOTermAndDescription(ref, alt, parser) {
     const soTerms = new Set();
     let descriptions = new Set();
     alt.forEach(a => {
-        let [soTerm, description] = getSOAndDescFromAltDefs(ref, a, parser);
+        let [soTerm, description] = getSOAndDescFromAltDefs(a, parser);
         if (!soTerm) {
             ;
             [soTerm, description] = getSOAndDescByExamination(ref, a);
@@ -58,7 +58,7 @@ function getSOTermAndDescription(ref, alt, parser) {
     return [];
 }
 exports.getSOTermAndDescription = getSOTermAndDescription;
-function getSOAndDescFromAltDefs(ref, alt, parser) {
+function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {
         return [];
     }
@@ -74,7 +74,7 @@ function getSOAndDescFromAltDefs(ref, alt, parser) {
     // try to look for a definition for a parent term if we can
     const modAlt = alt.split(':');
     if (modAlt.length > 1) {
-        return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, -1).join(':')}>`, parser);
+        return getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser);
     }
     // no parent
     return [];

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -3,7 +3,7 @@ import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
-export default class extends BaseFeatureDataAdapter {
+export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     private configured?;
     private configurePre;
     protected configure(): Promise<{

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -10,7 +10,7 @@ const tabix_1 = require("@gmod/tabix");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
 // local
 const VcfFeature_1 = __importDefault(require("../VcfFeature"));
-class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
+class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre() {
         const pm = this.pluginManager;
         const vcfGzLocation = this.getConf('vcfGzLocation');
@@ -71,4 +71,4 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-exports.default = default_1;
+exports.default = VcfTabixAdapter;

package/dist/VcfTabixAdapter/index.d.ts

@@ -1,4 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
 export { default as configSchema } from './configSchema';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VcfTabixAdapterF(pluginManager: PluginManager): void;

package/dist/VcfTabixAdapter/index.js

@@ -31,11 +31,12 @@ const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 const configSchema_1 = __importDefault(require("./configSchema"));
 var configSchema_2 = require("./configSchema");
 Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_2).default; } });
-exports.default = (pluginManager) => {
+function VcfTabixAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType_1.default({
         name: 'VcfTabixAdapter',
         displayName: 'VCF tabix adapter',
         configSchema: configSchema_1.default,
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfTabixAdapter'))).then(r => r.default),
     }));
-};
+}
+exports.default = VcfTabixAdapterF;

package/dist/extensionPoints.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/dist/extensionPoints.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const tracks_1 = require("@jbrowse/core/util/tracks");
-exports.default = (pluginManager) => {
+function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.vcf\.b?gz$/i;
@@ -47,4 +47,5 @@ exports.default = (pluginManager) => {
             return adapterGuesser(file, index, adapterHint);
         };
     });
-};
+}
+exports.default = ExtensionPointsF;

package/esm/ChordVariantDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ChordVariantDisplayF(pluginManager: PluginManager): void;

package/esm/ChordVariantDisplay/index.js

@@ -3,7 +3,7 @@ import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 // locals
 import configSchemaF from './models/configSchema';
 import stateModelF from './models/stateModelFactory';
-export default (pluginManager) => {
+export default function ChordVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);
         const stateModel = stateModelF(configSchema);
@@ -17,4 +17,4 @@ export default (pluginManager) => {
             ReactComponent: BaseChordDisplayComponent,
         });
     });
-};
+}

package/esm/LinearVariantDisplay/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearVariantDisplayF(pluginManager: PluginManager): void;

package/esm/LinearVariantDisplay/index.js

@@ -2,7 +2,7 @@ import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import stateModelFactory from './model';
 import configSchemaF from './configSchema';
-export default (pluginManager) => {
+export default function LinearVariantDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaF(pluginManager);
         return new DisplayType({
@@ -15,4 +15,4 @@ export default (pluginManager) => {
             ReactComponent: BaseLinearDisplayComponent,
         });
     });
-};
+}

package/esm/StructuralVariantChordRenderer/Chord.js

@@ -1,6 +1,6 @@
 import React, { useState } from 'react';
 import { observer } from 'mobx-react';
-import { polarToCartesian } from '@jbrowse/core/util';
+import { polarToCartesian, getStrokeProps } from '@jbrowse/core/util';
 import { readConfObject, } from '@jbrowse/core/configuration';
 import { parseBreakend } from '@gmod/vcf';
 function bpToRadians(block, pos) {
@@ -62,7 +62,7 @@ const Chord = observer(function Chord({ feature, blocksForRefs, radius, config,
         const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {
             feature,
         });
-        return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), stroke: hovered ? hoverStrokeColor : strokeColor, strokeWidth: hovered ? 3 : 1, onClick: evt => {
+        return (React.createElement("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), ...getStrokeProps(hovered ? hoverStrokeColor : strokeColor), strokeWidth: hovered ? 3 : 1, onClick: evt => {
                 if (endBlock && startBlock) {
                     onClick(feature, startBlock.region, endBlock.region, evt);
                 }

package/esm/StructuralVariantChordRenderer/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function StructuralVariantChordRendererF(pluginManager: PluginManager): void;

package/esm/StructuralVariantChordRenderer/index.js

@@ -1,7 +1,7 @@
 import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
 import configSchema from './configSchema';
 import ReactComponent from './ReactComponent';
-export default (pluginManager) => {
+export default function StructuralVariantChordRendererF(pluginManager) {
     pluginManager.addRendererType(() => new ChordRendererType({
         name: 'StructuralVariantChordRenderer',
         displayName: 'SV chord renderer',
@@ -9,4 +9,4 @@ export default (pluginManager) => {
         configSchema,
         pluginManager,
     }));
-};
+}

package/esm/VariantFeatureWidget/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VariantFeatureWidgetF(pluginManager: PluginManager): void;

package/esm/VariantFeatureWidget/index.js

@@ -2,7 +2,7 @@ import { lazy } from 'react';
 import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
 import { stateModelFactory } from './stateModelFactory';
 import { configSchema } from './configSchema';
-export default (pluginManager) => {
+export default function VariantFeatureWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType({
         name: 'VariantFeatureWidget',
         heading: 'Feature details',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         stateModel: stateModelFactory(pluginManager),
         ReactComponent: lazy(() => import('./VariantFeatureWidget')),
     }));
-};
+}

package/esm/VariantFeatureWidget/stateModelFactory.d.ts

@@ -11,6 +11,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
@@ -37,6 +48,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
@@ -46,6 +68,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/VariantTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function VariantTrackF(pm: PluginManager): void;

package/esm/VariantTrack/index.js

@@ -1,7 +1,7 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import configSchemaF from './configSchema';
-export default (pm) => {
+export default function VariantTrackF(pm) {
     pm.addTrackType(() => {
         const configSchema = configSchemaF(pm);
         return new TrackType({
@@ -11,4 +11,4 @@ export default (pm) => {
             stateModel: createBaseTrackModel(pm, 'VariantTrack', configSchema),
         });
     });
-};
+}

package/esm/VcfAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VcfAdapterF(pluginManager: PluginManager): void;

package/esm/VcfAdapter/index.js

@@ -1,10 +1,10 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function VcfAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'VcfAdapter',
         displayName: 'VCF adapter',
         configSchema,
         getAdapterClass: () => import('./VcfAdapter').then(r => r.default),
     }));
-};
+}

package/esm/VcfFeature/util.d.ts

@@ -3,5 +3,5 @@ import VCF from '@gmod/vcf';
  * Get a sequence ontology (SO) term that describes the variant type
  */
 export declare function getSOTermAndDescription(ref: string, alt: string[], parser: VCF): string[];
-export declare function getSOAndDescFromAltDefs(ref: string, alt: string, parser: VCF): string[];
+export declare function getSOAndDescFromAltDefs(alt: string, parser: VCF): string[];
 export declare function getSOAndDescByExamination(ref: string, alt: string): string[];

package/esm/VcfFeature/util.js

@@ -22,7 +22,7 @@ export function getSOTermAndDescription(ref, alt, parser) {
     const soTerms = new Set();
     let descriptions = new Set();
     alt.forEach(a => {
-        let [soTerm, description] = getSOAndDescFromAltDefs(ref, a, parser);
+        let [soTerm, description] = getSOAndDescFromAltDefs(a, parser);
         if (!soTerm) {
             ;
             [soTerm, description] = getSOAndDescByExamination(ref, a);
@@ -54,7 +54,7 @@ export function getSOTermAndDescription(ref, alt, parser) {
     }
     return [];
 }
-export function getSOAndDescFromAltDefs(ref, alt, parser) {
+export function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {
         return [];
     }
@@ -70,7 +70,7 @@ export function getSOAndDescFromAltDefs(ref, alt, parser) {
     // try to look for a definition for a parent term if we can
     const modAlt = alt.split(':');
     if (modAlt.length > 1) {
-        return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, -1).join(':')}>`, parser);
+        return getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser);
     }
     // no parent
     return [];

package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -3,7 +3,7 @@ import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
-export default class extends BaseFeatureDataAdapter {
+export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     private configured?;
     private configurePre;
     protected configure(): Promise<{

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -5,7 +5,7 @@ import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
 // local
 import VcfFeature from '../VcfFeature';
-export default class extends BaseFeatureDataAdapter {
+export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     async configurePre() {
         const pm = this.pluginManager;
         const vcfGzLocation = this.getConf('vcfGzLocation');

package/esm/VcfTabixAdapter/index.d.ts

@@ -1,4 +1,3 @@
 import PluginManager from '@jbrowse/core/PluginManager';
 export { default as configSchema } from './configSchema';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function VcfTabixAdapterF(pluginManager: PluginManager): void;

package/esm/VcfTabixAdapter/index.js

@@ -1,11 +1,11 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
 export { default as configSchema } from './configSchema';
-export default (pluginManager) => {
+export default function VcfTabixAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'VcfTabixAdapter',
         displayName: 'VCF tabix adapter',
         configSchema,
         getAdapterClass: () => import('./VcfTabixAdapter').then(r => r.default),
     }));
-};
+}

package/esm/extensionPoints.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/esm/extensionPoints.js

@@ -1,5 +1,5 @@
 import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
-export default (pluginManager) => {
+export default function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.vcf\.b?gz$/i;
@@ -45,4 +45,4 @@ export default (pluginManager) => {
             return adapterGuesser(file, index, adapterHint);
         };
     });
-};
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.10.3",
+  "version": "2.11.1",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -41,7 +41,7 @@
     "@gmod/tabix": "^1.5.6",
     "@gmod/vcf": "^5.0.9",
     "@mui/icons-material": "^5.0.2",
-    "@mui/x-data-grid": "^6.0.1",
+    "@mui/x-data-grid": "^7.0.0",
     "generic-filehandle": "^3.0.0"
   },
   "peerDependencies": {
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
+  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
 }