@jbrowse/plugin-variants 3.2.0 → 3.4.0

package/esm/VariantRPC/getGenotypeMatrix.js

@@ -1,27 +1,40 @@
 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, } = args;
+    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, } = args;
     const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
     const dataAdapter = adapter.dataAdapter;
-    const feats = await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray()));
     const genotypeFactor = new Set();
-    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter);
+    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()) {
+        for (const alt of Object.keys(alleleCounts)) {
             genotypeFactor.add(alt);
         }
     }
     const rows = {};
-    for (const { feature } of mafs) {
+    const cacheSplit = {};
+    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 alleles;
+            if (cacheSplit[val]) {
+                alleles = cacheSplit[val];
+            }
+            else {
+                alleles = val.split(/[/|]/);
+                cacheSplit[val] = alleles;
+            }
             let genotypeStatus = 0;
             let nonRefCount = 0;
             let uncalledCount = 0;
@@ -47,6 +60,6 @@ export async function getGenotypeMatrix({ pluginManager, args, }) {
             }
             rows[name].push(genotypeStatus);
         }
-    }
+    });
     return rows;
 }

package/esm/VariantRPC/types.d.ts

@@ -10,4 +10,27 @@ export interface GetGenotypeMatrixArgs {
     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/VcfAdapter/VcfAdapter.d.ts

@@ -31,6 +31,5 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     getSources(): Promise<{
         name: string;
     }[]>;
-    freeResources(): void;
 }
 export {};

package/esm/VcfAdapter/VcfAdapter.js

@@ -135,7 +135,6 @@ class VcfAdapter extends BaseFeatureDataAdapter {
                 .filter(f => s.has(f.name));
         }
     }
-    freeResources() { }
 }
 VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default VcfAdapter;

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',
@@ -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.d.ts

@@ -22,5 +22,4 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     getSources(): Promise<{
         name: string;
     }[]>;
-    freeResources(): void;
 }

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';
@@ -85,23 +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);
-            const ret = lines
+            const metadataLines = lines
                 .slice(1)
                 .filter(f => !!f)
                 .map(line => {
                 const [name, ...rest] = line.split('\t');
                 return {
-                    ...Object.fromEntries(rest.map((c, idx) => [header[idx + 1], c])),
+                    ...Object.fromEntries(header.slice(1).map((c, idx) => [c, rest[idx] || ''])),
                     name: name,
                 };
             });
-            const missing = ret.filter(f => !s.has(f.name));
-            if (missing.length) {
-                console.warn('Samples in metadata file not in VCF:', ret.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(',')));
             }
-            return ret.filter(f => s.has(f.name));
+            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/shared/MultiVariantBaseModel.d.ts

@@ -1,4 +1,4 @@
-import type { SampleInfo, Source } from '../shared/types';
+import type { SampleInfo, Source } from './types';
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
 import type { Instance } from 'mobx-state-tree';
@@ -90,6 +90,9 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
     renderingMode: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     autoHeight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    lengthCutoffFilter: import("mobx-state-tree").IType<number | undefined, number, number>;
+    jexlFilters: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>>;
+    referenceDrawingMode: import("mobx-state-tree").IType<string | undefined, string, string>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -202,7 +205,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -233,19 +236,28 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
     renderProps(): any;
 } & {
     sourcesLoadingStopToken: string | undefined;
+    simplifiedFeaturesStopToken: string | undefined;
     featureUnderMouseVolatile: Feature | undefined;
     sourcesVolatile: Source[] | undefined;
     featuresVolatile: Feature[] | undefined;
     hasPhased: boolean;
     sampleInfo: undefined | Record<string, SampleInfo>;
-    hoveredGenotype: string | undefined;
+    hoveredGenotype: {
+        genotype: string;
+        name: string;
+    } | undefined;
 } & {
+    setJexlFilters(f?: string[]): void;
     setRowHeight(arg: number): void;
-    setHoveredGenotype(arg: string): void;
+    setHoveredGenotype(arg?: {
+        genotype: string;
+        name: string;
+    }): void;
     setFeatures(f: Feature[]): void;
     setLayout(layout: Source[]): void;
     clearLayout(): void;
     setSourcesLoading(str: string): void;
+    setSimplifiedFeaturesLoading(str: string): void;
     setSources(sources: Source[]): void;
     setMafFilter(arg: number): void;
     setShowSidebarLabels(arg: boolean): void;
@@ -253,7 +265,9 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
     setAutoHeight(arg: boolean): void;
     setHasPhased(arg: boolean): void;
     setSampleInfo(arg: Record<string, SampleInfo>): void;
+    setReferenceDrawingMode(arg: string): void;
 } & {
+    readonly activeFilters: any;
     readonly preSources: Source[] | undefined;
     readonly sourcesWithoutLayout: {
         label: string;
@@ -274,6 +288,17 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
         HP?: number;
     }[] | undefined;
 } & {
+    readonly sourceMap: {
+        [k: string]: {
+            label: string;
+            id: string;
+            baseUri?: string;
+            name: string;
+            color?: string;
+            group?: string;
+            HP?: number;
+        };
+    } | undefined;
     readonly rowHeight: number;
     adapterProps(): any;
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
@@ -327,6 +352,18 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
         type?: undefined;
         checked?: undefined;
         onClick?: undefined;
+    } | {
+        label: string;
+        type: string;
+        subMenu: {
+            label: string;
+            type: string;
+            checked: boolean;
+            onClick: () => void;
+        }[];
+        icon?: undefined;
+        checked?: undefined;
+        onClick?: undefined;
     } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {