@jbrowse/plugin-variants 3.1.0 → 3.3.0

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -1,17 +1,9 @@
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { GetSimplifiedFeaturesArgs } from './types';
 import type { SampleInfo } from '../shared/types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
 export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
     name: string;
-    execute(args: {
-        adapterConfig: AnyConfigurationModel;
-        stopToken?: string;
-        sessionId: string;
-        headers?: Record<string, string>;
-        regions: Region[];
-        bpPerPx: number;
-    }, rpcDriverClassName: string): Promise<{
+    execute(args: GetSimplifiedFeaturesArgs, rpcDriverClassName: string): Promise<{
         hasPhased: boolean;
         sampleInfo: Record<string, SampleInfo>;
         features: {
@@ -20,6 +12,7 @@ export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWith
                 start: number;
                 end: number;
                 refName: string;
+                name: any;
             };
         }[];
     }>;

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -1,5 +1,6 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { forEachWithStopTokenCheck } from '@jbrowse/core/util';
 import { firstValueFrom, toArray } from 'rxjs';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
 export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
@@ -8,18 +9,21 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
         this.name = 'MultiVariantGetSimplifiedFeatures';
     }
     async execute(args, rpcDriverClassName) {
-        var _a, _b;
-        const pm = this.pluginManager;
         const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { minorAlleleFrequencyFilter, regions, adapterConfig, sessionId } = deserializedArgs;
-        const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
-        const feats = await firstValueFrom(dataAdapter
-            .getFeaturesInMultipleRegions(regions, deserializedArgs)
-            .pipe(toArray()));
-        const features = getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter);
+        const { lengthCutoffFilter, minorAlleleFrequencyFilter, regions, adapterConfig, stopToken, sessionId, } = deserializedArgs;
+        const { dataAdapter } = await getAdapter(this.pluginManager, sessionId, adapterConfig);
+        const features = getFeaturesThatPassMinorAlleleFrequencyFilter({
+            minorAlleleFrequencyFilter,
+            lengthCutoffFilter,
+            stopToken,
+            features: await firstValueFrom(dataAdapter
+                .getFeaturesInMultipleRegions(regions, deserializedArgs)
+                .pipe(toArray())),
+        });
         const sampleInfo = {};
         let hasPhased = false;
-        for (const { feature } of features) {
+        forEachWithStopTokenCheck(features, stopToken, ({ feature }) => {
+            var _a, _b;
             const samp = feature.get('genotypes');
             for (const [key, val] of Object.entries(samp)) {
                 const isPhased = val.includes('|');
@@ -29,7 +33,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
                     isPhased: ((_b = sampleInfo[key]) === null || _b === void 0 ? void 0 : _b.isPhased) || isPhased,
                 };
             }
-        }
+        });
         return {
             hasPhased,
             sampleInfo,
@@ -39,6 +43,7 @@ export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersA
                     start: feature.get('start'),
                     end: feature.get('end'),
                     refName: feature.get('refName'),
+                    name: feature.get('name'),
                 },
             })),
         };

package/esm/VariantRPC/getGenotypeMatrix.d.ts

@@ -0,0 +1,6 @@
+import type { GetGenotypeMatrixArgs } from './types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+export declare function getGenotypeMatrix({ pluginManager, args, }: {
+    pluginManager: PluginManager;
+    args: GetGenotypeMatrixArgs;
+}): Promise<Record<string, number[]>>;

package/esm/VariantRPC/getGenotypeMatrix.js

@@ -0,0 +1,57 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { forEachWithStopTokenCheck } from '@jbrowse/core/util';
+import { firstValueFrom, toArray } from 'rxjs';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
+export async function getGenotypeMatrix({ pluginManager, args, }) {
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, } = args;
+    const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
+    const dataAdapter = adapter.dataAdapter;
+    const genotypeFactor = new Set();
+    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter({
+        minorAlleleFrequencyFilter,
+        lengthCutoffFilter,
+        stopToken,
+        features: await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())),
+    });
+    for (const { alleleCounts } of mafs) {
+        for (const alt of alleleCounts.keys()) {
+            genotypeFactor.add(alt);
+        }
+    }
+    const rows = {};
+    forEachWithStopTokenCheck(mafs, stopToken, ({ feature }) => {
+        const genotypes = feature.get('genotypes');
+        for (const { name } of sources) {
+            if (!rows[name]) {
+                rows[name] = [];
+            }
+            const val = genotypes[name];
+            const alleles = val.split(/[/|]/);
+            let genotypeStatus = 0;
+            let nonRefCount = 0;
+            let uncalledCount = 0;
+            for (const l of alleles) {
+                if (l === '.') {
+                    uncalledCount++;
+                }
+                else if (l !== '0') {
+                    nonRefCount++;
+                }
+            }
+            if (uncalledCount === alleles.length) {
+                genotypeStatus = -1;
+            }
+            else if (nonRefCount === 0) {
+                genotypeStatus = 0;
+            }
+            else if (nonRefCount === alleles.length) {
+                genotypeStatus = 2;
+            }
+            else {
+                genotypeStatus = 1;
+            }
+            rows[name].push(genotypeStatus);
+        }
+    });
+    return rows;
+}

package/esm/VariantRPC/types.d.ts

@@ -0,0 +1,36 @@
+import type { Source } from '../shared/types';
+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 {
+    adapterConfig: AnyConfigurationModel;
+    stopToken?: string;
+    sessionId: string;
+    headers?: Record<string, string>;
+    regions: Region[];
+    bpPerPx: number;
+    minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
+}
+export interface ClusterGenotypeMatrixArgs {
+    adapterConfig: AnyConfigurationModel;
+    stopToken?: string;
+    statusCallback: (arg: string) => void;
+    sessionId: string;
+    headers?: Record<string, string>;
+    regions: Region[];
+    bpPerPx: number;
+    sources: Source[];
+    minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
+}

package/esm/VariantRPC/types.js

@@ -0,0 +1 @@
+export {};

package/esm/VcfAdapter/VcfAdapter.js

@@ -1,7 +1,7 @@
 import IntervalTree from '@flatten-js/interval-tree';
 import VcfParser from '@gmod/vcf';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzip, getProgressDisplayStr } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import VcfFeature from '../VcfFeature';
@@ -45,7 +45,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
                 }
             }
             if (i++ % 10000 === 0) {
-                statusCallback(`Loading ${Math.floor(blockStart / 1000000).toLocaleString('en-US')}/${Math.floor(buffer.length / 1000000).toLocaleString('en-US')} MB`);
+                statusCallback(`Loading ${getProgressDisplayStr(blockStart, buffer.length)}`);
             }
             blockStart = n + 1;
         }
@@ -96,9 +96,12 @@ class VcfAdapter extends BaseFeatureDataAdapter {
             try {
                 const { start, end, refName } = region;
                 const { intervalTreeMap } = await this.setup();
-                (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([start, end]).forEach(f => {
+                for (const f of ((_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
+                    start,
+                    end,
+                ])) || []) {
                     observer.next(f);
-                });
+                }
                 observer.complete();
             }
             catch (e) {

package/esm/VcfFeature/index.js

@@ -10,7 +10,6 @@ function dataFromVariant(variant, parser) {
         description,
         type,
         name: ID === null || ID === void 0 ? void 0 : ID.join(','),
-        aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
     };
 }
 function getEnd(variant) {

package/esm/VcfFeature/util.d.ts

@@ -2,3 +2,5 @@ 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[];
+export declare function getMinimalDesc(ref: string, alt: string): string;
+export declare function makeSimpleAltString(genotype: string, ref: string, alt: string[]): string;

package/esm/VcfFeature/util.js

@@ -1,4 +1,5 @@
 import { parseBreakend } from '@gmod/vcf';
+import { getBpDisplayStr } from '@jbrowse/core/util';
 const altTypeToSO = {
     DEL: 'deletion',
     INS: 'insertion',
@@ -17,7 +18,7 @@ export function getSOTermAndDescription(ref, alt, parser) {
     }
     const soTerms = new Set();
     let descriptions = new Set();
-    alt.forEach(a => {
+    for (const a of alt) {
         let [soTerm, description] = getSOAndDescFromAltDefs(a, parser);
         if (!soTerm) {
             ;
@@ -27,7 +28,7 @@ export function getSOTermAndDescription(ref, alt, parser) {
             soTerms.add(soTerm);
             descriptions.add(description);
         }
-    });
+    }
     if (descriptions.size > 1) {
         const descs = [...descriptions];
         const prefixes = new Set(descs
@@ -62,63 +63,158 @@ export function getSOAndDescFromAltDefs(alt, parser) {
         return [soTerm, alt];
     }
     const modAlt = alt.split(':');
-    if (modAlt.length > 1) {
-        return getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser);
-    }
-    return [];
+    return modAlt.length > 1
+        ? getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser)
+        : [];
 }
 export function getSOAndDescByExamination(ref, alt) {
     const bnd = parseBreakend(alt);
     if (bnd) {
         return ['breakend', alt];
     }
-    if (ref.length === 1 && alt.length === 1) {
+    else if (ref.length === 1 && alt.length === 1) {
         return ['SNV', makeDescriptionString('SNV', ref, alt)];
     }
-    if (alt === '<INS>') {
+    else if (alt === '<INS>') {
         return ['insertion', alt];
     }
-    if (alt === '<DEL>') {
+    else if (alt === '<DEL>') {
         return ['deletion', alt];
     }
-    if (alt === '<DUP>') {
+    else if (alt === '<DUP>') {
         return ['duplication', alt];
     }
-    if (alt === '<CNV>') {
+    else if (alt === '<CNV>') {
         return ['cnv', alt];
     }
-    if (alt === '<INV>') {
+    else if (alt === '<INV>') {
         return ['inversion', alt];
     }
-    if (alt === '<TRA>') {
+    else if (alt === '<TRA>') {
         return ['translocation', alt];
     }
-    if (alt.includes('<')) {
+    else if (alt.includes('<')) {
         return ['sv', alt];
     }
-    if (ref.length === alt.length) {
-        return ref.split('').reverse().join('') === alt
-            ? ['inversion', makeDescriptionString('inversion', ref, alt)]
-            : ['substitution', makeDescriptionString('substitution', ref, alt)];
+    else if (ref.length === alt.length) {
+        const lenRef = ref.length;
+        const lenAlt = alt.length;
+        if (lenRef > 5 || lenAlt > 5) {
+            const lena = getBpDisplayStr(lenRef);
+            const lenb = getBpDisplayStr(lenAlt);
+            return ref.split('').reverse().join('') === alt
+                ? ['inverson', makeDescriptionString('inv', lena, lenb)]
+                : ['substitution', makeDescriptionString('substitution', lena, lenb)];
+        }
+        else {
+            return ref.split('').reverse().join('') === alt
+                ? ['inversion', makeDescriptionString('inv', ref, alt)]
+                : ['substitution', makeDescriptionString('substitution', ref, alt)];
+        }
     }
-    if (ref.length <= alt.length) {
+    else if (ref.length <= alt.length) {
         const len = alt.length - ref.length;
-        const lena = len.toLocaleString('en-US');
+        const lenAlt = alt.length;
+        const lenRef = ref.length;
+        const lena = getBpDisplayStr(len);
         return [
             'insertion',
-            len > 5 ? `${lena}bp INS` : makeDescriptionString('insertion', ref, alt),
+            lenRef > 5 || lenAlt > 5
+                ? `${lena} INS`
+                : makeDescriptionString('insertion', len > 5 ? lena : ref, alt),
         ];
     }
-    if (ref.length > alt.length) {
-        const len = ref.length - alt.length;
-        const lena = len.toLocaleString('en-US');
+    else if (ref.length > alt.length) {
+        const lenRef = ref.length;
+        const lenAlt = alt.length;
+        const lena = getBpDisplayStr(lenRef - lenAlt);
         return [
             'deletion',
-            len > 5 ? `${lena}bp DEL` : makeDescriptionString('deletion', ref, alt),
+            lenRef > 5 || lenAlt > 5
+                ? `${lena} DEL`
+                : makeDescriptionString('deletion', ref, alt),
         ];
     }
-    return ['indel', makeDescriptionString('indel', ref, alt)];
+    else {
+        return ['indel', makeDescriptionString('indel', ref, alt)];
+    }
+}
+export function getMinimalDesc(ref, alt) {
+    const bnd = parseBreakend(alt);
+    if (bnd) {
+        return alt;
+    }
+    else if (ref.length === 1 && alt.length === 1) {
+        return alt;
+    }
+    else if (alt === '<INS>') {
+        return alt;
+    }
+    else if (alt === '<DEL>') {
+        return alt;
+    }
+    else if (alt === '<DUP>') {
+        return alt;
+    }
+    else if (alt === '<CNV>') {
+        return alt;
+    }
+    else if (alt === '<INV>') {
+        return alt;
+    }
+    else if (alt === '<TRA>') {
+        return alt;
+    }
+    else if (alt.includes('<')) {
+        return alt;
+    }
+    else if (ref.length === alt.length) {
+        const lenRef = ref.length;
+        const lenAlt = alt.length;
+        if (lenRef > 5 || lenAlt > 5) {
+            const lena = getBpDisplayStr(lenRef);
+            const lenb = getBpDisplayStr(lenAlt);
+            return ref.split('').reverse().join('') === alt
+                ? makeDescriptionString('inv', lena, lenb)
+                : makeDescriptionString('substitution', lena, lenb);
+        }
+        else {
+            return ref.split('').reverse().join('') === alt
+                ? makeDescriptionString('inv', ref, alt)
+                : makeDescriptionString('substitution', ref, alt);
+        }
+    }
+    else if (ref.length <= alt.length) {
+        const len = alt.length - ref.length;
+        const lenAlt = alt.length;
+        const lenRef = ref.length;
+        const lena = getBpDisplayStr(len);
+        return lenRef > 5 || lenAlt > 5
+            ? `${lena} INS`
+            : makeDescriptionString('insertion', len > 5 ? lena : ref, alt);
+    }
+    else if (ref.length > alt.length) {
+        const lenRef = ref.length;
+        const lenAlt = alt.length;
+        const lena = getBpDisplayStr(lenRef - lenAlt);
+        return lenRef > 5 || lenAlt > 5
+            ? `${lena} DEL`
+            : makeDescriptionString('deletion', ref, alt);
+    }
+    else {
+        return makeDescriptionString('indel', ref, alt);
+    }
 }
 function makeDescriptionString(soTerm, ref, alt) {
-    return `${soTerm} ${ref} -> ${alt}`;
+    return `${soTerm} ${[ref, alt].join(' -> ')}`;
+}
+export function makeSimpleAltString(genotype, ref, alt) {
+    return genotype
+        .split(/[/|]/)
+        .map(r => r === '.'
+        ? '.'
+        : +r === 0
+            ? `ref(${ref.length < 10 ? ref : getBpDisplayStr(ref.length)})`
+            : getMinimalDesc(ref, alt[+r - 1] || ''))
+        .join(genotype.includes('|') ? '|' : '/');
 }

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -1,7 +1,7 @@
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { fetchAndMaybeUnzipText, updateStatus } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzipText, shorten2, updateStatus, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import VcfFeature from '../VcfFeature';
@@ -85,17 +85,27 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
             const lines = txt.split(/\n|\r\n|\r/);
             const header = lines[0].split('\t');
             const { parser } = await this.configure();
-            const s = new Set(parser.samples);
-            return lines
+            const metadataLines = lines
                 .slice(1)
+                .filter(f => !!f)
                 .map(line => {
-                const cols = line.split('\t');
+                const [name, ...rest] = line.split('\t');
                 return {
-                    name: cols[0],
-                    ...Object.fromEntries(cols.slice(1).map((c, idx) => [header[idx + 1], c])),
+                    ...Object.fromEntries(header.slice(1).map((c, idx) => [c, rest[idx] || ''])),
+                    name: name,
                 };
-            })
-                .filter(f => s.has(f.name));
+            });
+            const vcfSampleSet = new Set(parser.samples);
+            const metadataSet = new Set(metadataLines.map(r => r.name));
+            const metadataNotInVcfSamples = [...metadataSet].filter(f => !vcfSampleSet.has(f));
+            const vcfSamplesNotInMetadata = [...vcfSampleSet].filter(f => !metadataSet.has(f));
+            if (metadataNotInVcfSamples.length) {
+                console.warn(`There are ${metadataNotInVcfSamples.length} samples in metadata file (${metadataLines.length} lines) not in VCF (${parser.samples.length} samples):`, shorten2(metadataNotInVcfSamples.join(',')));
+            }
+            if (vcfSamplesNotInMetadata.length) {
+                console.warn(`There are ${vcfSamplesNotInMetadata.length} samples in VCF file (${parser.samples.length} samples) not in metadata file (${metadataLines.length} lines):`, shorten2(vcfSamplesNotInMetadata.map(m => m).join(',')));
+            }
+            return metadataLines.filter(f => vcfSampleSet.has(f.name));
         }
     }
     freeResources() { }

package/esm/getMultiVariantFeaturesAutorun.d.ts

@@ -6,6 +6,7 @@ export declare function getMultiVariantFeaturesAutorun(self: {
     adapterConfig: AnyConfigurationModel;
     sources?: Source[];
     minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
     statsReadyAndRegionNotTooLarge: boolean;
     adapterProps: () => Record<string, unknown>;
     setError: (error: unknown) => void;
@@ -13,4 +14,5 @@ export declare function getMultiVariantFeaturesAutorun(self: {
     setMessage: (str: string) => void;
     setHasPhased: (arg: boolean) => void;
     setSampleInfo: (arg: Record<string, SampleInfo>) => void;
+    setSimplifiedFeaturesLoading: (arg: string) => void;
 }): void;

package/esm/getMultiVariantFeaturesAutorun.js

@@ -1,5 +1,6 @@
 import { SimpleFeature, getContainingView, getSession, } from '@jbrowse/core/util';
 import { isAbortException } from '@jbrowse/core/util/aborting';
+import { createStopToken } from '@jbrowse/core/util/stopToken';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { autorun } from 'mobx';
 import { addDisposer, isAlive } from 'mobx-state-tree';
@@ -10,16 +11,20 @@ export function getMultiVariantFeaturesAutorun(self) {
             if (!view.initialized || !self.statsReadyAndRegionNotTooLarge) {
                 return;
             }
+            const stopToken = createStopToken();
+            self.setSimplifiedFeaturesLoading(stopToken);
             const { rpcManager } = getSession(self);
-            const { sources, minorAlleleFrequencyFilter, adapterConfig } = self;
+            const { lengthCutoffFilter, sources, minorAlleleFrequencyFilter, adapterConfig, } = self;
             if (sources) {
                 const sessionId = getRpcSessionId(self);
                 const { sampleInfo, hasPhased, features } = (await rpcManager.call(sessionId, 'MultiVariantGetSimplifiedFeatures', {
                     regions: view.dynamicBlocks.contentBlocks,
                     sources,
                     minorAlleleFrequencyFilter,
+                    lengthCutoffFilter,
                     sessionId,
                     adapterConfig,
+                    stopToken,
                 }));
                 if (isAlive(self)) {
                     self.setHasPhased(hasPhased);
@@ -34,5 +39,7 @@ export function getMultiVariantFeaturesAutorun(self) {
                 getSession(self).notifyError(`${e}`, e);
             }
         }
-    }, { delay: 1000 }));
+    }, {
+        delay: 1000,
+    }));
 }

package/esm/getMultiVariantSourcesAutorun.js

@@ -13,12 +13,13 @@ export function getMultiVariantSourcesAutorun(self) {
             }
             const { rpcManager } = getSession(self);
             const { adapterConfig } = self;
-            const token = createStopToken();
-            self.setSourcesLoading(token);
+            const stopToken = createStopToken();
+            self.setSourcesLoading(stopToken);
             const sessionId = getRpcSessionId(self);
             const sources = (await rpcManager.call(sessionId, 'MultiVariantGetSources', {
                 sessionId,
                 adapterConfig,
+                stopToken,
             }));
             if (isAlive(self)) {
                 self.setSources(sources);

package/esm/index.js

@@ -8,6 +8,7 @@ import MultiVariantRendererF from './MultiLinearVariantRenderer';
 import SplitVcfTabixAdapterF from './SplitVcfTabixAdapter';
 import StructuralVariantChordRendererF from './StructuralVariantChordRenderer';
 import VariantFeatureWidgetF from './VariantFeatureWidget';
+import { MultiVariantClusterGenotypeMatrix } from './VariantRPC/MultiVariantClusterGenotypeMatrix';
 import { MultiVariantGetGenotypeMatrix } from './VariantRPC/MultiVariantGetGenotypeMatrix';
 import { MultiVariantGetSimplifiedFeatures } from './VariantRPC/MultiVariantGetSimplifiedFeatures';
 import { MultiVariantGetSources } from './VariantRPC/MultiVariantGetSources';
@@ -36,6 +37,7 @@ export default class VariantsPlugin extends Plugin {
         ChordVariantDisplayF(pluginManager);
         pluginManager.addRpcMethod(() => new MultiVariantGetSources(pluginManager));
         pluginManager.addRpcMethod(() => new MultiVariantGetGenotypeMatrix(pluginManager));
+        pluginManager.addRpcMethod(() => new MultiVariantClusterGenotypeMatrix(pluginManager));
         pluginManager.addRpcMethod(() => new MultiVariantGetSimplifiedFeatures(pluginManager));
     }
 }