@jbrowse/plugin-variants 2.16.1 → 2.18.0

package/dist/VariantRPC/MultiVariantGetSources.js

@@ -0,0 +1,22 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.MultiVariantGetSources = void 0;
+const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
+class MultiVariantGetSources extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
+    constructor() {
+        super(...arguments);
+        this.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 (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
+        return dataAdapter.getSources(regions, deserializedArgs);
+    }
+}
+exports.MultiVariantGetSources = MultiVariantGetSources;

package/dist/VariantTrack/configSchema.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+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<{
     name: {
         description: string;
         type: string;
@@ -77,4 +77,3 @@ declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/c
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;
-export default configSchema;

package/dist/VariantTrack/configSchema.js

@@ -1,17 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = VariantTrackF;
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-/**
- * #config VariantTrack
- * Mostly similar to feature track, but has `ChordDisplayType` registered to it,
- * and custom feature details in `LinearVariantDisplay`
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const configSchema = (pluginManager) => (0, configuration_1.ConfigurationSchema)('VariantTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
-    baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
-});
-exports.default = configSchema;
+function VariantTrackF(pluginManager) {
+    return (0, configuration_1.ConfigurationSchema)('VariantTrack', {}, {
+        baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
+    });
+}

package/dist/VariantTrack/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function VariantTrackF(pm: PluginManager): void;

package/dist/VcfAdapter/VcfAdapter.d.ts

@@ -1,6 +1,7 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 type StatusCallback = (arg: string) => void;
 export default class VcfAdapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;

package/dist/VcfAdapter/VcfAdapter.js

@@ -3,14 +3,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+const vcf_1 = __importDefault(require("@gmod/vcf"));
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-const vcf_1 = __importDefault(require("@gmod/vcf"));
-// local
 const VcfFeature_1 = __importDefault(require("../VcfFeature"));
 class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
@@ -28,20 +26,17 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     async setupP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await (0, io_1.openLocation)(this.getConf('vcfLocation'), this.pluginManager).readFile(opts));
-        const buffer = (0, util_1.isGzip)(buf)
-            ? await (0, util_1.updateStatus)('Unzipping', statusCallback, () => (0, bgzf_filehandle_1.unzip)(buf))
-            : buf;
+        const loc = (0, io_1.openLocation)(this.getConf('vcfLocation'), this.pluginManager);
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
-        const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+        const decoder = new TextDecoder('utf8');
         let i = 0;
         while (blockStart < buffer.length) {
             const n = buffer.indexOf('\n', blockStart);
-            // could be a non-newline ended file, so slice to end of file if n===-1
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
-            const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+            const line = decoder.decode(b).trim();
             if (line) {
                 if (line.startsWith('#')) {
                     headerLines.push(line);
@@ -114,7 +109,7 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/dist/VcfAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     vcfLocation: {
         type: string;
         defaultValue: {

package/dist/VcfAdapter/configSchema.js

@@ -1,14 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config VcfAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const VcfAdapter = (0, configuration_1.ConfigurationSchema)('VcfAdapter', {
-    /**
-     * #slot
-     */
     vcfLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },

package/dist/VcfAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function VcfAdapterF(pluginManager: PluginManager): void;

package/dist/VcfFeature/index.d.ts

@@ -1,43 +1,19 @@
-import { Feature } from '@jbrowse/core/util';
-import VCF from '@gmod/vcf';
-type Samples = Record<string, Record<string, {
-    values: string[] | number[] | null;
-}>>;
-interface FeatureData {
-    [key: string]: unknown;
-    refName: string;
-    start: number;
-    end: number;
-    description?: string;
-    type?: string;
-    name?: string;
-    aliases?: string[];
-    samples?: Samples;
-}
+import type VCFParser from '@gmod/vcf';
+import type { Variant } from '@gmod/vcf';
+import type { Feature } from '@jbrowse/core/util';
 export default class VCFFeature implements Feature {
     private variant;
     private parser;
     private data;
     private _id;
     constructor(args: {
-        variant: any;
-        parser: VCF;
+        variant: Variant;
+        parser: VCFParser;
         id: string;
     });
     get(field: string): any;
-    set(): void;
     parent(): undefined;
     children(): undefined;
-    tags(): string[];
     id(): string;
-    dataFromVariant(variant: {
-        REF: string;
-        POS: number;
-        ALT?: string[];
-        CHROM: string;
-        INFO: any;
-        ID?: string[];
-    }): FeatureData;
     toJSON(): any;
 }
-export {};

package/dist/VcfFeature/index.js

@@ -1,55 +1,64 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-// locals
 const util_1 = require("./util");
+function dataFromVariant(variant, parser) {
+    const { REF = '', ALT, POS, CHROM, ID } = variant;
+    const start = POS - 1;
+    const [type, description] = (0, util_1.getSOTermAndDescription)(REF, ALT, parser);
+    return {
+        refName: CHROM,
+        start,
+        end: getEnd(variant),
+        description,
+        type,
+        name: ID === null || ID === void 0 ? void 0 : ID.join(','),
+        aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
+    };
+}
+function getEnd(variant) {
+    const { POS, REF = '', ALT } = variant;
+    const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.includes('<TRA>');
+    const start = POS - 1;
+    const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
+    if (isSymbolic) {
+        const info = variant.INFO;
+        if (info.END && !isTRA) {
+            return +info.END[0];
+        }
+    }
+    return start + REF.length;
+}
 class VCFFeature {
     constructor(args) {
         this.variant = args.variant;
         this.parser = args.parser;
-        this.data = this.dataFromVariant(this.variant);
+        this.data = dataFromVariant(this.variant, this.parser);
         this._id = args.id;
     }
     get(field) {
         var _a;
         return field === 'samples'
-            ? this.variant.SAMPLES
-            : ((_a = this.data[field]) !== null && _a !== void 0 ? _a : this.variant[field]);
+            ? this.variant.SAMPLES()
+            : field === 'genotypes'
+                ? this.variant.GENOTYPES()
+                : ((_a = this.data[field]) !== null && _a !== void 0 ? _a : this.variant[field]);
     }
-    set() { }
     parent() {
         return undefined;
     }
     children() {
         return undefined;
     }
-    tags() {
-        return [...Object.keys(this.data), ...Object.keys(this.variant), 'samples'];
-    }
     id() {
         return this._id;
     }
-    dataFromVariant(variant) {
-        const { REF, ALT, POS, CHROM, INFO, ID } = variant;
-        const start = POS - 1;
-        const [type, description] = (0, util_1.getSOTermAndDescription)(REF, ALT, this.parser);
-        const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.includes('<TRA>');
-        const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
-        return {
-            refName: CHROM,
-            start,
-            end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,
-            description,
-            type,
-            name: ID === null || ID === void 0 ? void 0 : ID.join(','),
-            aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
-        };
-    }
     toJSON() {
+        const { SAMPLES, GENOTYPES, ...rest } = this.variant;
         return {
             uniqueId: this._id,
-            ...this.variant,
+            ...rest,
             ...this.data,
-            samples: this.variant.SAMPLES,
+            samples: this.variant.SAMPLES(),
         };
     }
 }

package/dist/VcfFeature/util.d.ts

@@ -1,7 +1,4 @@
-import VCF from '@gmod/vcf';
-/**
- * Get a sequence ontology (SO) term that describes the variant type
- */
+import type VCF from '@gmod/vcf';
 export declare function getSOTermAndDescription(ref: string, alt: string[] | undefined, 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

@@ -16,11 +16,7 @@ const altTypeToSO = {
     NON_REF: 'sequence_variant',
     '*': 'sequence_variant',
 };
-/**
- * Get a sequence ontology (SO) term that describes the variant type
- */
 function getSOTermAndDescription(ref, alt, parser) {
-    // it's just a remark if there are no alternate alleles
     if (!alt || alt.length === 0) {
         return ['remark', 'no alternative alleles'];
     }
@@ -37,7 +33,6 @@ function getSOTermAndDescription(ref, alt, parser) {
             descriptions.add(description);
         }
     });
-    // Combine descriptions like ["SNV G -> A", "SNV G -> T"] to ["SNV G -> A,T"]
     if (descriptions.size > 1) {
         const descs = [...descriptions];
         const prefixes = new Set(descs
@@ -65,26 +60,19 @@ function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {
         return [];
     }
-    // look for a definition with an SO type for this
     let soTerm = altTypeToSO[alt];
-    // if no SO term but ALT is in metadata, assume sequence_variant
     if (!soTerm && parser.getMetadata('ALT', alt)) {
         soTerm = 'sequence_variant';
     }
     if (soTerm) {
         return [soTerm, alt];
     }
-    // try to look for a definition for a parent term if we can
     const modAlt = alt.split(':');
     if (modAlt.length > 1) {
         return getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser);
     }
-    // no parent
     return [];
 }
-// note: term SNV is used instead of SNP because SO definition of SNP says
-// abundance must be at least 1% in population, and can't be sure we meet
-// that
 function getSOAndDescByExamination(ref, alt) {
     const bnd = (0, vcf_1.parseBreakend)(alt);
     if (bnd) {

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -1,8 +1,9 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     private configured?;
     private configurePre;
@@ -14,5 +15,8 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     getHeader(): Promise<string>;
     getMetadata(): Promise<any>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getSources(): Promise<{
+        name: string;
+    }[]>;
     freeResources(): void;
 }

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -3,12 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const tabix_1 = require("@gmod/tabix");
+const vcf_1 = __importDefault(require("@gmod/vcf"));
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const tabix_1 = require("@gmod/tabix");
-const vcf_1 = __importDefault(require("@gmod/vcf"));
-// local
 const VcfFeature_1 = __importDefault(require("../VcfFeature"));
 class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre() {
@@ -66,8 +65,14 @@ class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 ...opts,
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
+    }
+    async getSources() {
+        const { parser } = await this.configure();
+        return parser.samples.map(name => ({
+            name,
+        }));
     }
-    freeResources( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = VcfTabixAdapter;

package/dist/VcfTabixAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     vcfGzLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configuration
         };
     };
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.location
-         */
         location: {
             type: string;
             defaultValue: {

package/dist/VcfTabixAdapter/configSchema.js

@@ -1,31 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config VcfTabixAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const mobx_state_tree_1 = require("mobx-state-tree");
+function x() { }
 const VcfTabixAdapter = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapter', {
-    /**
-     * #slot
-     */
     vcfGzLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
     },
     index: (0, configuration_1.ConfigurationSchema)('VcfIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {

package/dist/VcfTabixAdapter/index.d.ts

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

package/dist/configSchema.d.ts

@@ -0,0 +1,34 @@
+declare const WiggleRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default WiggleRenderer;

package/dist/configSchema.js

@@ -0,0 +1,44 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function x() { }
+const WiggleRenderer = (0, configuration_1.ConfigurationSchema)('WiggleRenderer', {
+    color: {
+        type: 'color',
+        description: 'the color of track, overrides posColor and negColor',
+        defaultValue: '#f0f',
+    },
+    posColor: {
+        type: 'color',
+        description: 'the color to use when the score is positive',
+        defaultValue: 'blue',
+    },
+    negColor: {
+        type: 'color',
+        description: 'the color to use when the score is negative',
+        defaultValue: 'red',
+    },
+    clipColor: {
+        type: 'color',
+        description: 'the color of the clipping marker',
+        defaultValue: 'red',
+    },
+    bicolorPivot: {
+        type: 'stringEnum',
+        model: mobx_state_tree_1.types.enumeration('Scale type', [
+            'numeric',
+            'mean',
+            'z_score',
+            'none',
+        ]),
+        description: 'type of bicolor pivot',
+        defaultValue: 'numeric',
+    },
+    bicolorPivotValue: {
+        type: 'number',
+        defaultValue: 0,
+        description: 'value to use for bicolor pivot',
+    },
+}, { explicitlyTyped: true });
+exports.default = WiggleRenderer;

package/dist/extensionPoints.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/dist/getMultiVariantFeaturesAutorun.d.ts

@@ -0,0 +1,19 @@
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
+export interface Source {
+    name: string;
+    color?: string;
+    group?: string;
+    [key: string]: string | undefined;
+}
+export declare function getMultiVariantFeaturesAutorun(self: {
+    configuration: AnyConfigurationModel;
+    adapterConfig: AnyConfigurationModel;
+    sources?: Source[];
+    mafFilter: number;
+    statsReadyAndRegionNotTooLarge: boolean;
+    adapterProps: () => Record<string, unknown>;
+    setError: (error: unknown) => void;
+    setFeatures: (f: Feature[]) => void;
+    setMessage: (str: string) => void;
+}): void;

package/dist/getMultiVariantFeaturesAutorun.js

@@ -0,0 +1,40 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getMultiVariantFeaturesAutorun = getMultiVariantFeaturesAutorun;
+const util_1 = require("@jbrowse/core/util");
+const aborting_1 = require("@jbrowse/core/util/aborting");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function getMultiVariantFeaturesAutorun(self) {
+    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
+        try {
+            const view = (0, util_1.getContainingView)(self);
+            if (!view.initialized || !self.statsReadyAndRegionNotTooLarge) {
+                return;
+            }
+            const { rpcManager } = (0, util_1.getSession)(self);
+            const { sources, mafFilter, adapterConfig } = self;
+            if (!sources) {
+                return;
+            }
+            const sessionId = (0, tracks_1.getRpcSessionId)(self);
+            const features = (await rpcManager.call(sessionId, 'MultiVariantGetSimplifiedFeatures', {
+                regions: view.dynamicBlocks.contentBlocks,
+                sources,
+                mafFilter,
+                sessionId,
+                adapterConfig,
+            }));
+            if ((0, mobx_state_tree_1.isAlive)(self)) {
+                self.setFeatures(features.map(f => new util_1.SimpleFeature(f)));
+            }
+        }
+        catch (e) {
+            if (!(0, aborting_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(self)) {
+                console.error(e);
+                (0, util_1.getSession)(self).notifyError(`${e}`, e);
+            }
+        }
+    }, { delay: 1000 }));
+}

package/dist/getMultiVariantSourcesAutorun.d.ts

@@ -0,0 +1,16 @@
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export interface Source {
+    name: string;
+    color?: string;
+    group?: string;
+    [key: string]: string | undefined;
+}
+export declare function getMultiVariantSourcesAutorun(self: {
+    configuration: AnyConfigurationModel;
+    adapterConfig: AnyConfigurationModel;
+    adapterProps: () => Record<string, unknown>;
+    setSourcesLoading: (aborter: string) => void;
+    setError: (error: unknown) => void;
+    setMessage: (str: string) => void;
+    setSources: (sources: Source[]) => void;
+}): void;