@jbrowse/plugin-variants 4.1.1 → 4.1.4

package/esm/PlinkLDAdapter/configSchemaTabix.d.ts

@@ -1,4 +1,4 @@
-declare const PlinkLDTabixAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const PlinkLDTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     ldLocation: {
         type: string;
         defaultValue: {
@@ -6,7 +6,7 @@ declare const PlinkLDTabixAdapter: import("node_modules/@jbrowse/core/src/config
             locationType: string;
         };
     };
-    index: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         indexType: {
             model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             type: string;
@@ -19,6 +19,6 @@ declare const PlinkLDTabixAdapter: import("node_modules/@jbrowse/core/src/config
                 locationType: string;
             };
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default PlinkLDTabixAdapter;

package/esm/SplitVcfTabixAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const SplitVcfTabixAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const SplitVcfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     vcfGzLocationMap: {
         type: string;
         defaultValue: {};
@@ -19,5 +19,5 @@ declare const SplitVcfTabixAdapter: import("node_modules/@jbrowse/core/src/confi
             locationType: string;
         };
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default SplitVcfTabixAdapter;

package/esm/StructuralVariantChordRenderer/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const configSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     strokeColor: {
         type: string;
         description: string;
@@ -17,5 +17,5 @@ declare const configSchema: import("node_modules/@jbrowse/core/src/configuration
         defaultValue: string;
         contextVariable: string[];
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/VariantFeatureWidget/configSchema.d.ts

@@ -1 +1 @@
-export declare const configSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/esm/VariantFeatureWidget/stateModelFactory.d.ts

@@ -33,7 +33,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         readonly hasExon: boolean | undefined;
         readonly hasExonOrCDS: boolean | undefined;
     } & {
-        afterAttach(): void;
+        afterCreate(): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
     descriptions: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 } & {
@@ -84,7 +84,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         readonly hasExon: boolean | undefined;
         readonly hasExonOrCDS: boolean | undefined;
     } & {
-        afterAttach(): void;
+        afterCreate(): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
     descriptions: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized, {

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -1,11 +1,14 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { createStopTokenChecker } from '@jbrowse/core/util/stopToken';
 import { getGenotypeMatrix } from "./getGenotypeMatrix.js";
 export class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name = 'MultiVariantGetGenotypeMatrix';
     async execute(args, rpcDriverClassName) {
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const stopTokenCheck = createStopTokenChecker(deserializedArgs.stopToken);
         return getGenotypeMatrix({
             pluginManager: this.pluginManager,
-            args: await this.deserializeArguments(args, rpcDriverClassName),
+            args: { ...deserializedArgs, stopTokenCheck },
         });
     }
 }

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -8,6 +8,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
     async execute(args, rpcDriverClassName) {
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
         const { lengthCutoffFilter, minorAlleleFrequencyFilter, regions, adapterConfig, stopToken, sessionId, } = deserializedArgs;
+        const stopTokenCheck = createStopTokenChecker(stopToken);
         const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
         const rawFeatures = await firstValueFrom(dataAdapter
             .getFeaturesInMultipleRegions(regions, deserializedArgs)
@@ -15,11 +16,10 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
         const sampleInfo = {};
         const genotypesCache = new Map();
         let hasPhased = false;
-        const lastCheck = createStopTokenChecker(stopToken);
         const features = getFeaturesThatPassMinorAlleleFrequencyFilter({
             minorAlleleFrequencyFilter,
             lengthCutoffFilter,
-            lastCheck,
+            stopTokenCheck,
             features: rawFeatures,
             genotypesCache,
         });
@@ -47,7 +47,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
                     isPhased: existing?.isPhased || isPhased,
                 };
             }
-            checkStopToken2(lastCheck);
+            checkStopToken2(stopTokenCheck);
         }
         return {
             hasPhased,

package/esm/VariantRPC/executeClusterGenotypeMatrix.js

@@ -1,14 +1,17 @@
 import { clusterData, toNewick } from '@gmod/hclust';
+import { createStopTokenChecker } from '@jbrowse/core/util/stopToken';
 import { getGenotypeMatrix } from "./getGenotypeMatrix.js";
 import { getPhasedGenotypeMatrix } from "./getPhasedGenotypeMatrix.js";
 export async function executeClusterGenotypeMatrix({ pluginManager, args, }) {
-    const { renderingMode, sampleInfo } = args;
+    const { renderingMode, sampleInfo, stopToken } = args;
+    const stopTokenCheck = createStopTokenChecker(stopToken);
+    const argsWithCheck = { ...args, stopTokenCheck };
     const matrix = renderingMode === 'phased' && sampleInfo
         ? await getPhasedGenotypeMatrix({
             pluginManager,
-            args: { ...args, sampleInfo },
+            args: { ...argsWithCheck, sampleInfo },
         })
-        : await getGenotypeMatrix({ pluginManager, args });
+        : await getGenotypeMatrix({ pluginManager, args: argsWithCheck });
     const sampleLabels = Object.keys(matrix);
     const result = await clusterData({
         data: Object.values(matrix),

package/esm/VariantRPC/getGenotypeMatrix.d.ts

@@ -1,13 +1,12 @@
 import type { Source } from '../shared/types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-import type { StopToken } from '@jbrowse/core/util/stopToken';
+import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
 export declare function getGenotypeMatrix({ pluginManager, args, }: {
     pluginManager: PluginManager;
     args: {
         adapterConfig: AnyConfigurationModel;
-        stopToken?: StopToken;
+        stopTokenCheck?: LastStopTokenCheck;
         sessionId: string;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/VariantRPC/getGenotypeMatrix.js

@@ -1,11 +1,10 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
 const SPLITTER = /[/|]/;
 export async function getGenotypeMatrix({ pluginManager, args, }) {
-    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, } = args;
-    const lastCheck = createStopTokenChecker(stopToken);
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopTokenCheck, } = args;
     const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
     const rows = Object.fromEntries(sources.map(s => [s.name, []]));
@@ -13,7 +12,7 @@ export async function getGenotypeMatrix({ pluginManager, args, }) {
     const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter({
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
-        lastCheck,
+        stopTokenCheck,
         splitCache,
         features: await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())),
     });
@@ -42,7 +41,7 @@ export async function getGenotypeMatrix({ pluginManager, args, }) {
                         : 1;
             rows[name].push(genotypeStatus);
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     return rows;
 }

package/esm/VariantRPC/getLDMatrix.d.ts

@@ -1,7 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-import type { StopToken } from '@jbrowse/core/util/stopToken';
+import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
 export type LDMetric = 'r2' | 'dprime';
 export interface FilterStats {
     totalVariants: number;
@@ -32,7 +31,7 @@ export declare function getLDMatrix({ pluginManager, args, }: {
     pluginManager: PluginManager;
     args: {
         adapterConfig: AnyConfigurationModel;
-        stopToken?: StopToken;
+        stopTokenCheck?: LastStopTokenCheck;
         sessionId: string;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/VariantRPC/getLDMatrix.js

@@ -1,6 +1,6 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
 const SPLITTER = /[/|]/;
@@ -206,8 +206,7 @@ function calculateLDStats(geno1, geno2, signedLD = false) {
     return { r2: signedLD ? r : r2, dprime };
 }
 export async function getLDMatrix({ pluginManager, args, }) {
-    const { minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, hweFilterThreshold = 0.001, callRateFilter = 0, jexlFilters = [], stopToken, ldMetric = 'r2', signedLD = false, } = args;
-    const lastCheck = createStopTokenChecker(stopToken);
+    const { minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, hweFilterThreshold = 0.001, callRateFilter = 0, jexlFilters = [], stopTokenCheck, ldMetric = 'r2', signedLD = false, } = args;
     const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
     const sources = await dataAdapter.getSources(regions);
@@ -238,7 +237,7 @@ export async function getLDMatrix({ pluginManager, args, }) {
     const filteredFeatures = getFeaturesThatPassMinorAlleleFrequencyFilter({
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
-        lastCheck,
+        stopTokenCheck,
         splitCache,
         features: rawFeatures,
     });
@@ -339,7 +338,7 @@ export async function getLDMatrix({ pluginManager, args, }) {
         if (dataIsPhased) {
             phasedHaplotypes.push(encodePhasedHaplotypes(genotypes, samples));
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     const n = snps.length;
     const ldSize = (n * (n - 1)) / 2;
@@ -352,7 +351,7 @@ export async function getLDMatrix({ pluginManager, args, }) {
                 : calculateLDStats(encodedGenotypes[i], encodedGenotypes[j], signedLD);
             ldValues[idx++] = ldMetric === 'dprime' ? stats.dprime : stats.r2;
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     const filterStats = {
         totalVariants,

package/esm/VariantRPC/getPhasedGenotypeMatrix.d.ts

@@ -1,13 +1,12 @@
 import type { SampleInfo, Source } from '../shared/types.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-import type { StopToken } from '@jbrowse/core/util/stopToken';
+import type { LastStopTokenCheck, Region } from '@jbrowse/core/util';
 export declare function getPhasedGenotypeMatrix({ pluginManager, args, }: {
     pluginManager: PluginManager;
     args: {
         adapterConfig: AnyConfigurationModel;
-        stopToken?: StopToken;
+        stopTokenCheck?: LastStopTokenCheck;
         sessionId: string;
         headers?: Record<string, string>;
         regions: Region[];

package/esm/VariantRPC/getPhasedGenotypeMatrix.js

@@ -1,10 +1,9 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
 export async function getPhasedGenotypeMatrix({ pluginManager, args, }) {
-    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, sampleInfo, } = args;
-    const lastCheck = createStopTokenChecker(stopToken);
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopTokenCheck, sampleInfo, } = args;
     const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
     const rows = {};
@@ -19,7 +18,7 @@ export async function getPhasedGenotypeMatrix({ pluginManager, args, }) {
     const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter({
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
-        lastCheck,
+        stopTokenCheck,
         splitCache,
         features: await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())),
     });
@@ -44,7 +43,7 @@ export async function getPhasedGenotypeMatrix({ pluginManager, args, }) {
                 }
             }
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     return rows;
 }

package/esm/VariantTrack/configSchema.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-export default function VariantTrackF(pluginManager: PluginManager): import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function VariantTrackF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;
         type: string;
@@ -31,7 +31,7 @@ export default function VariantTrackF(pluginManager: PluginManager): import("nod
         defaultValue: string;
     };
     adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
-    textSearching: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         indexingAttributes: {
             type: string;
             description: string;
@@ -43,9 +43,9 @@ export default function VariantTrackF(pluginManager: PluginManager): import("nod
             defaultValue: string[];
         };
         textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
-    formatDetails: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         feature: {
             type: string;
             description: string;
@@ -68,8 +68,8 @@ export default function VariantTrackF(pluginManager: PluginManager): import("nod
             defaultValue: number;
             description: string;
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {
             type: string;
             description: string;
@@ -80,5 +80,5 @@ export default function VariantTrackF(pluginManager: PluginManager): import("nod
             type: string;
             defaultValue: boolean;
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;

package/esm/VcfAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const VcfAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     vcfLocation: {
         type: string;
         defaultValue: {
@@ -14,5 +14,5 @@ declare const VcfAdapter: import("node_modules/@jbrowse/core/src/configuration/c
             locationType: string;
         };
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfAdapter;

package/esm/VcfTabixAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const VcfTabixAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     vcfGzLocation: {
         type: string;
         defaultValue: {
@@ -6,7 +6,7 @@ declare const VcfTabixAdapter: import("node_modules/@jbrowse/core/src/configurat
             locationType: string;
         };
     };
-    index: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         indexType: {
             model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             type: string;
@@ -19,7 +19,7 @@ declare const VcfTabixAdapter: import("node_modules/@jbrowse/core/src/configurat
                 locationType: string;
             };
         };
-    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     samplesTsvLocation: {
         type: string;
         defaultValue: {
@@ -28,5 +28,5 @@ declare const VcfTabixAdapter: import("node_modules/@jbrowse/core/src/configurat
             locationType: string;
         };
     };
-}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfTabixAdapter;