@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/esm/VariantFeatureWidget/stateModelFactory.d.ts

@@ -1,17 +1,17 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-import type { Instance } from 'mobx-state-tree';
-export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    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<{}, {
+import type { Instance } from '@jbrowse/mobx-state-tree';
+export declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    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>;
+    formattedFields: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+    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>;
+    view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    track: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    trackId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    trackType: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    maxDepth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{}, {
         showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
@@ -34,11 +34,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
+    }, 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>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
-    descriptions: import("mobx-state-tree").IType<any, any, any>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
+    descriptions: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
 }, {
     error: unknown;
 } & {
@@ -51,18 +51,18 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     afterCreate(): void;
 }, {
     type: "BaseFeatureWidget";
-} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    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<{}, {
+} & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    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>;
+    formattedFields: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+    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>;
+    view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    track: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    trackId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    trackType: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    maxDepth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{}, {
         showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
@@ -85,20 +85,20 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
-}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    type: "BaseFeatureWidget";
+    }, 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, {
+    track: import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined;
+    view: import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined;
     id: string;
-    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    type: "BaseFeatureWidget";
     trackId: string | undefined;
+    sequenceFeatureDetails: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{}>;
+    descriptions: Record<string, unknown> | undefined;
+    formattedFields: any;
     trackType: string | undefined;
     maxDepth: number | undefined;
-    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
-    formattedFields: any;
-    descriptions: Record<string, unknown> | undefined;
     finalizedFeatureData: any;
-} & import("mobx-state-tree")._NotCustomized>;
+} & import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
 export type VariantFeatureWidgetModel = Instance<VariantFeatureWidgetStateModel>;

package/esm/VariantFeatureWidget/stateModelFactory.js

@@ -1,5 +1,5 @@
 import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 export function stateModelFactory(pluginManager) {
     const baseModel = baseModelFactory(pluginManager);
     return types.compose(baseModel, types.model('VariantFeatureWidget', {

package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.d.ts

@@ -1,14 +1,9 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { ClusterGenotypeMatrixArgs } from './types';
+import type { ClusterGenotypeMatrixArgs } from './types.ts';
 export declare class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
     execute(args: ClusterGenotypeMatrixArgs, rpcDriverClassName: string): Promise<{
-        clusters: {
-            height: number;
-            indexes: number[];
-        } | undefined;
-        distances: number[][];
         order: number[];
-        clustersGivenK: number[][][];
+        tree: string;
     }>;
 }

package/esm/VariantRPC/MultiVariantClusterGenotypeMatrix.js

@@ -1,23 +1,12 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import { clusterData } from '@jbrowse/core/util/cluster';
-import { getGenotypeMatrix } from './getGenotypeMatrix';
 export class MultiVariantClusterGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
-    constructor() {
-        super(...arguments);
-        this.name = 'MultiVariantClusterGenotypeMatrix';
-    }
+    name = 'MultiVariantClusterGenotypeMatrix';
     async execute(args, rpcDriverClassName) {
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const matrix = await getGenotypeMatrix({
+        const { executeClusterGenotypeMatrix } = await import("./executeClusterGenotypeMatrix.js");
+        return executeClusterGenotypeMatrix({
             pluginManager: this.pluginManager,
             args: deserializedArgs,
         });
-        return clusterData({
-            data: Object.values(matrix),
-            stopToken: deserializedArgs.stopToken,
-            onProgress: progress => {
-                deserializedArgs.statusCallback(progress);
-            },
-        });
     }
 }

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts

@@ -1,6 +1,8 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { GetGenotypeMatrixArgs } from './types';
+import type { GetGenotypeMatrixArgs } from './types.ts';
 export declare class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: GetGenotypeMatrixArgs, rpcDriverClassName: string): Promise<Record<string, number[]>>;
+    execute(args: GetGenotypeMatrixArgs, rpcDriverClassName: string): Promise<{
+        [k: string]: number[];
+    }>;
 }

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -1,10 +1,7 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import { getGenotypeMatrix } from './getGenotypeMatrix';
+import { getGenotypeMatrix } from "./getGenotypeMatrix.js";
 export class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
-    constructor() {
-        super(...arguments);
-        this.name = 'MultiVariantGetGenotypeMatrix';
-    }
+    name = 'MultiVariantGetGenotypeMatrix';
     async execute(args, rpcDriverClassName) {
         return getGenotypeMatrix({
             pluginManager: this.pluginManager,

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -1,6 +1,6 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import type { GetSimplifiedFeaturesArgs } from './types';
-import type { SampleInfo } from '../shared/types';
+import type { GetSimplifiedFeaturesArgs } from './types.ts';
+import type { SampleInfo } from '../shared/types.ts';
 export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
     execute(args: GetSimplifiedFeaturesArgs, rpcDriverClassName: string): Promise<{

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -1,39 +1,54 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
-import { forEachWithStopTokenCheck } from '@jbrowse/core/util';
+import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom, toArray } from 'rxjs';
-import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from "../shared/minorAlleleFrequencyUtils.js";
 export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
-    constructor() {
-        super(...arguments);
-        this.name = 'MultiVariantGetSimplifiedFeatures';
-    }
+    name = 'MultiVariantGetSimplifiedFeatures';
     async execute(args, rpcDriverClassName) {
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
         const { lengthCutoffFilter, minorAlleleFrequencyFilter, regions, adapterConfig, stopToken, sessionId, } = deserializedArgs;
         const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
+        const rawFeatures = await firstValueFrom(dataAdapter
+            .getFeaturesInMultipleRegions(regions, deserializedArgs)
+            .pipe(toArray()));
+        const sampleInfo = {};
+        const genotypesCache = new Map();
+        let hasPhased = false;
+        const lastCheck = createStopTokenChecker(stopToken);
         const features = getFeaturesThatPassMinorAlleleFrequencyFilter({
             minorAlleleFrequencyFilter,
             lengthCutoffFilter,
-            stopToken,
-            features: await firstValueFrom(dataAdapter
-                .getFeaturesInMultipleRegions(regions, deserializedArgs)
-                .pipe(toArray())),
+            lastCheck,
+            features: rawFeatures,
+            genotypesCache,
         });
-        const sampleInfo = {};
-        let hasPhased = false;
-        forEachWithStopTokenCheck(features, stopToken, ({ feature }) => {
-            var _a, _b;
-            const samp = feature.get('genotypes');
+        for (const { feature } of features) {
+            const featureId = feature.id();
+            let samp = genotypesCache.get(featureId);
+            if (!samp) {
+                samp = feature.get('genotypes');
+                genotypesCache.set(featureId, samp);
+            }
             for (const [key, val] of Object.entries(samp)) {
                 const isPhased = val.includes('|');
-                hasPhased || (hasPhased = isPhased);
+                hasPhased ||= isPhased;
+                let ploidy = 1;
+                if (isPhased) {
+                    for (const char of val) {
+                        if (char === '|') {
+                            ploidy++;
+                        }
+                    }
+                }
+                const existing = sampleInfo[key];
                 sampleInfo[key] = {
-                    maxPloidy: Math.max(((_a = sampleInfo[key]) === null || _a === void 0 ? void 0 : _a.maxPloidy) || 0, val.split('|').length),
-                    isPhased: ((_b = sampleInfo[key]) === null || _b === void 0 ? void 0 : _b.isPhased) || isPhased,
+                    maxPloidy: Math.max(existing?.maxPloidy ?? 0, ploidy),
+                    isPhased: existing?.isPhased || isPhased,
                 };
             }
-        });
+            checkStopToken2(lastCheck);
+        }
         return {
             hasPhased,
             sampleInfo,

package/esm/VariantRPC/MultiVariantGetSources.js

@@ -1,15 +1,11 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
 export class MultiVariantGetSources extends RpcMethodTypeWithFiltersAndRenameRegions {
-    constructor() {
-        super(...arguments);
-        this.name = 'MultiVariantGetSources';
-    }
+    name = 'MultiVariantGetSources';
     async execute(args, rpcDriverClassName) {
-        const pm = this.pluginManager;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
         const { regions, adapterConfig, sessionId } = deserializedArgs;
-        const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
+        const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
         return dataAdapter.getSources(regions, deserializedArgs);
     }
 }

package/esm/VariantRPC/executeClusterGenotypeMatrix.d.ts

@@ -0,0 +1,22 @@
+import type { Source } from '../shared/types.ts';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region, StopToken } from '@jbrowse/core/util';
+export declare function executeClusterGenotypeMatrix({ pluginManager, args, }: {
+    pluginManager: PluginManager;
+    args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: StopToken;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+        minorAlleleFrequencyFilter: number;
+        lengthCutoffFilter: number;
+        statusCallback: (arg: string) => void;
+        sources: Source[];
+    };
+}): Promise<{
+    order: number[];
+    tree: string;
+}>;

package/esm/VariantRPC/executeClusterGenotypeMatrix.js

@@ -0,0 +1,19 @@
+import { clusterData, toNewick } from '@gmod/hclust';
+import { getGenotypeMatrix } from "./getGenotypeMatrix.js";
+export async function executeClusterGenotypeMatrix({ pluginManager, args, }) {
+    const matrix = await getGenotypeMatrix({
+        pluginManager,
+        args,
+    });
+    const sampleLabels = Object.keys(matrix);
+    const result = await clusterData({
+        data: Object.values(matrix),
+        sampleLabels,
+        stopToken: args.stopToken,
+        onProgress: args.statusCallback,
+    });
+    return {
+        order: result.order,
+        tree: toNewick(result.tree),
+    };
+}

package/esm/VariantRPC/getGenotypeMatrix.d.ts

@@ -1,6 +1,21 @@
-import type { GetGenotypeMatrixArgs } from './types';
+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';
 export declare function getGenotypeMatrix({ pluginManager, args, }: {
     pluginManager: PluginManager;
-    args: GetGenotypeMatrixArgs;
-}): Promise<Record<string, number[]>>;
+    args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: StopToken;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sources: Source[];
+        bpPerPx: number;
+        minorAlleleFrequencyFilter: number;
+        lengthCutoffFilter: number;
+    };
+}): Promise<{
+    [k: string]: number[];
+}>;

package/esm/VariantRPC/getGenotypeMatrix.js

@@ -1,65 +1,48 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { forEachWithStopTokenCheck } from '@jbrowse/core/util';
+import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
 import { firstValueFrom, toArray } from 'rxjs';
-import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
+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 adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
-    const genotypeFactor = new Set();
+    const rows = Object.fromEntries(sources.map(s => [s.name, []]));
+    const splitCache = {};
     const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter({
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
-        stopToken,
+        lastCheck,
+        splitCache,
         features: await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())),
     });
-    for (const { alleleCounts } of mafs) {
-        for (const alt of Object.keys(alleleCounts)) {
-            genotypeFactor.add(alt);
-        }
-    }
-    const rows = {};
-    const cacheSplit = {};
-    forEachWithStopTokenCheck(mafs, stopToken, ({ feature }) => {
+    for (const { feature } of mafs) {
         const genotypes = feature.get('genotypes');
         for (const { name } of sources) {
-            if (!rows[name]) {
-                rows[name] = [];
-            }
             const val = genotypes[name];
-            let alleles;
-            if (cacheSplit[val]) {
-                alleles = cacheSplit[val];
-            }
-            else {
-                alleles = val.split(/[/|]/);
-                cacheSplit[val] = alleles;
-            }
-            let genotypeStatus = 0;
+            const alleles = splitCache[val] ?? (splitCache[val] = val.split(SPLITTER));
             let nonRefCount = 0;
             let uncalledCount = 0;
-            for (const l of alleles) {
-                if (l === '.') {
+            for (let i = 0, l = alleles.length; i < l; i++) {
+                const allele = alleles[i];
+                if (allele === '.') {
                     uncalledCount++;
                 }
-                else if (l !== '0') {
+                else if (allele !== '0') {
                     nonRefCount++;
                 }
             }
-            if (uncalledCount === alleles.length) {
-                genotypeStatus = -1;
-            }
-            else if (nonRefCount === 0) {
-                genotypeStatus = 0;
-            }
-            else if (nonRefCount === alleles.length) {
-                genotypeStatus = 2;
-            }
-            else {
-                genotypeStatus = 1;
-            }
+            const genotypeStatus = uncalledCount === alleles.length
+                ? -1
+                : nonRefCount === 0
+                    ? 0
+                    : nonRefCount === alleles.length
+                        ? 2
+                        : 1;
             rows[name].push(genotypeStatus);
         }
-    });
+        checkStopToken2(lastCheck);
+    }
     return rows;
 }

package/esm/VariantRPC/types.d.ts

@@ -1,20 +1,9 @@
-import type { Source } from '../shared/types';
+import type { Source } from '../shared/types.ts';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-export interface GetGenotypeMatrixArgs {
-    sources: Source[];
-    minorAlleleFrequencyFilter: number;
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
-    lengthCutoffFilter: number;
-}
-export interface GetSimplifiedFeaturesArgs {
+import type { Region, StopToken } from '@jbrowse/core/util';
+interface BaseVariantRpcArgs {
     adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
+    stopToken?: StopToken;
     sessionId: string;
     headers?: Record<string, string>;
     regions: Region[];
@@ -22,15 +11,12 @@ export interface GetSimplifiedFeaturesArgs {
     minorAlleleFrequencyFilter: number;
     lengthCutoffFilter: number;
 }
-export interface ClusterGenotypeMatrixArgs {
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
+export interface GetGenotypeMatrixArgs extends BaseVariantRpcArgs {
+    sources: Source[];
+}
+export type GetSimplifiedFeaturesArgs = BaseVariantRpcArgs;
+export interface ClusterGenotypeMatrixArgs extends BaseVariantRpcArgs {
     statusCallback: (arg: string) => void;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
     sources: Source[];
-    minorAlleleFrequencyFilter: number;
-    lengthCutoffFilter: number;
 }
+export {};

package/esm/VariantTrack/configSchema.d.ts

@@ -1,5 +1,5 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-export default function VariantTrackF(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+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<{
     name: {
         description: string;
         type: string;
@@ -25,8 +25,13 @@ export default function VariantTrackF(pluginManager: PluginManager): import("@jb
         description: string;
         defaultValue: {};
     };
-    adapter: import("mobx-state-tree").IAnyModelType;
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    rpcDriverName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    adapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    textSearching: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         indexingAttributes: {
             type: string;
             description: string;
@@ -37,10 +42,10 @@ export default function VariantTrackF(pluginManager: PluginManager): import("@jb
             description: string;
             defaultValue: string[];
         };
-        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyModelType;
+    }, import("node_modules/@jbrowse/core/src/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<{
         feature: {
             type: string;
             description: string;
@@ -63,8 +68,8 @@ export default function VariantTrackF(pluginManager: PluginManager): import("@jb
             defaultValue: number;
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         config: {
             type: string;
             description: string;
@@ -75,5 +80,5 @@ export default function VariantTrackF(pluginManager: PluginManager): import("@jb
             type: string;
             defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;

package/esm/VariantTrack/index.js

@@ -1,6 +1,7 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
-import configSchemaF from './configSchema';
+import configSchemaF from "./configSchema.js";
+import { stringifyVCF } from "./saveTrackFormats/vcf.js";
 export default function VariantTrackF(pm) {
     pm.addTrackType(() => {
         const configSchema = configSchemaF(pm);
@@ -8,7 +9,17 @@ export default function VariantTrackF(pm) {
             name: 'VariantTrack',
             displayName: 'Variant track',
             configSchema,
-            stateModel: createBaseTrackModel(pm, 'VariantTrack', configSchema),
+            stateModel: createBaseTrackModel(pm, 'VariantTrack', configSchema).views(() => ({
+                saveTrackFileFormatOptions() {
+                    return {
+                        vcf: {
+                            name: 'VCF',
+                            extension: 'vcf',
+                            callback: stringifyVCF,
+                        },
+                    };
+                },
+            })),
         });
     });
 }

package/esm/VariantTrack/saveTrackFormats/vcf.d.ts

@@ -0,0 +1,4 @@
+import type { Feature } from '@jbrowse/core/util';
+export declare function stringifyVCF({ features }: {
+    features: Feature[];
+}): string;

package/esm/VariantTrack/saveTrackFormats/vcf.js

@@ -0,0 +1,15 @@
+function generateINFO(feature) {
+    return Object.entries(feature.get('INFO'))
+        .map(([key, value]) => `${key}=${value}`)
+        .join(';');
+}
+export function stringifyVCF({ features }) {
+    const fields = ['refName', 'start', 'name', 'REF', 'ALT', 'QUAL', 'FILTER'];
+    return features
+        .map(feature => {
+        return `${fields
+            .map(field => feature.get(field) || '.')
+            .join('\t')}\t${generateINFO(feature)}`;
+    })
+        .join('\n');
+}