@jbrowse/plugin-variants 3.2.0 → 3.4.0

package/dist/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/dist/VcfAdapter/VcfAdapter.d.ts

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

package/dist/VcfAdapter/VcfAdapter.js

@@ -140,7 +140,6 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 .filter(f => s.has(f.name));
         }
     }
-    freeResources() { }
 }
 VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = VcfAdapter;

package/dist/VcfFeature/index.js

@@ -12,7 +12,6 @@ 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/dist/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/dist/VcfFeature/util.js

@@ -3,7 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.getSOTermAndDescription = getSOTermAndDescription;
 exports.getSOAndDescFromAltDefs = getSOAndDescFromAltDefs;
 exports.getSOAndDescByExamination = getSOAndDescByExamination;
+exports.getMinimalDesc = getMinimalDesc;
+exports.makeSimpleAltString = makeSimpleAltString;
 const vcf_1 = require("@gmod/vcf");
+const util_1 = require("@jbrowse/core/util");
 const altTypeToSO = {
     DEL: 'deletion',
     INS: 'insertion',
@@ -67,63 +70,158 @@ 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)
+        : [];
 }
 function getSOAndDescByExamination(ref, alt) {
     const bnd = (0, vcf_1.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 = (0, util_1.getBpDisplayStr)(lenRef);
+            const lenb = (0, util_1.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 = (0, util_1.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 = (0, util_1.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)];
+    }
+}
+function getMinimalDesc(ref, alt) {
+    const bnd = (0, vcf_1.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 = (0, util_1.getBpDisplayStr)(lenRef);
+            const lenb = (0, util_1.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 = (0, util_1.getBpDisplayStr)(len);
+        return lenRef > 5 || lenAlt > 5
+            ? `${lena} INS`
+            : makeDescriptionString('insertion', len > 5 ? lena : ref, alt);
+    }
+    else if (ref.length > alt.length) {
+        const lenRef = ref.length;
+        const lenAlt = alt.length;
+        const lena = (0, util_1.getBpDisplayStr)(lenRef - lenAlt);
+        return lenRef > 5 || lenAlt > 5
+            ? `${lena} DEL`
+            : makeDescriptionString('deletion', ref, alt);
+    }
+    else {
+        return makeDescriptionString('indel', ref, alt);
+    }
 }
 function makeDescriptionString(soTerm, ref, alt) {
-    return `${soTerm} ${ref} -> ${alt}`;
+    return `${soTerm} ${[ref, alt].join(' -> ')}`;
+}
+function makeSimpleAltString(genotype, ref, alt) {
+    return genotype
+        .split(/[/|]/)
+        .map(r => r === '.'
+        ? '.'
+        : +r === 0
+            ? `ref(${ref.length < 10 ? ref : (0, util_1.getBpDisplayStr)(ref.length)})`
+            : getMinimalDesc(ref, alt[+r - 1] || ''))
+        .join(genotype.includes('|') ? '|' : '/');
 }

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

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

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -90,24 +90,28 @@ class VcfTabixAdapter extends BaseAdapter_1.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):`, (0, util_1.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):`, (0, util_1.shorten2)(vcfSamplesNotInMetadata.map(m => m).join(',')));
+            }
+            return metadataLines.filter(f => vcfSampleSet.has(f.name));
         }
     }
-    freeResources() { }
 }
 exports.default = VcfTabixAdapter;

package/dist/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/dist/getMultiVariantFeaturesAutorun.js

@@ -3,6 +3,7 @@ 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 stopToken_1 = require("@jbrowse/core/util/stopToken");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
@@ -13,16 +14,20 @@ function getMultiVariantFeaturesAutorun(self) {
             if (!view.initialized || !self.statsReadyAndRegionNotTooLarge) {
                 return;
             }
+            const stopToken = (0, stopToken_1.createStopToken)();
+            self.setSimplifiedFeaturesLoading(stopToken);
             const { rpcManager } = (0, util_1.getSession)(self);
-            const { sources, minorAlleleFrequencyFilter, adapterConfig } = self;
+            const { lengthCutoffFilter, sources, minorAlleleFrequencyFilter, adapterConfig, } = self;
             if (sources) {
                 const sessionId = (0, tracks_1.getRpcSessionId)(self);
                 const { sampleInfo, hasPhased, features } = (await rpcManager.call(sessionId, 'MultiVariantGetSimplifiedFeatures', {
                     regions: view.dynamicBlocks.contentBlocks,
                     sources,
                     minorAlleleFrequencyFilter,
+                    lengthCutoffFilter,
                     sessionId,
                     adapterConfig,
+                    stopToken,
                 }));
                 if ((0, mobx_state_tree_1.isAlive)(self)) {
                     self.setHasPhased(hasPhased);
@@ -37,5 +42,7 @@ function getMultiVariantFeaturesAutorun(self) {
                 (0, util_1.getSession)(self).notifyError(`${e}`, e);
             }
         }
-    }, { delay: 1000 }));
+    }, {
+        delay: 1000,
+    }));
 }

package/dist/getMultiVariantSourcesAutorun.js

@@ -16,12 +16,13 @@ function getMultiVariantSourcesAutorun(self) {
             }
             const { rpcManager } = (0, util_1.getSession)(self);
             const { adapterConfig } = self;
-            const token = (0, stopToken_1.createStopToken)();
-            self.setSourcesLoading(token);
+            const stopToken = (0, stopToken_1.createStopToken)();
+            self.setSourcesLoading(stopToken);
             const sessionId = (0, tracks_1.getRpcSessionId)(self);
             const sources = (await rpcManager.call(sessionId, 'MultiVariantGetSources', {
                 sessionId,
                 adapterConfig,
+                stopToken,
             }));
             if ((0, mobx_state_tree_1.isAlive)(self)) {
                 self.setSources(sources);

package/dist/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">> & {

package/dist/shared/MultiVariantBaseModel.js

@@ -39,6 +39,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = MultiVariantBaseModelF;
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
+const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
 const util_1 = require("@jbrowse/core/util");
 const stopToken_1 = require("@jbrowse/core/util/stopToken");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
@@ -52,7 +53,8 @@ const mobx_state_tree_1 = require("mobx-state-tree");
 const getSources_1 = require("./getSources");
 const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetColorDialog'))));
 const MAFFilterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/MAFFilterDialog'))));
-const ClusterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ClusterDialog/ClusterDialog'))));
+const AddFiltersDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/AddFiltersDialog'))));
+const ClusterDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/MultiVariantClusterDialog/ClusterDialog'))));
 const SetRowHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetRowHeightDialog'))));
 function MultiVariantBaseModelF(configSchema) {
     return mobx_state_tree_1.types
@@ -60,14 +62,18 @@ function MultiVariantBaseModelF(configSchema) {
         type: mobx_state_tree_1.types.literal('LinearVariantMatrixDisplay'),
         layout: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), []),
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        minorAlleleFrequencyFilter: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0.1),
+        minorAlleleFrequencyFilter: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 0),
         showSidebarLabelsSetting: true,
         renderingMode: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, 'alleleCount'),
         rowHeightSetting: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 8),
         autoHeight: true,
+        lengthCutoffFilter: Number.MAX_SAFE_INTEGER,
+        jexlFilters: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string)),
+        referenceDrawingMode: 'skip',
     }))
         .volatile(() => ({
         sourcesLoadingStopToken: undefined,
+        simplifiedFeaturesStopToken: undefined,
         featureUnderMouseVolatile: undefined,
         sourcesVolatile: undefined,
         featuresVolatile: undefined,
@@ -76,6 +82,9 @@ function MultiVariantBaseModelF(configSchema) {
         hoveredGenotype: undefined,
     }))
         .actions(self => ({
+        setJexlFilters(f) {
+            self.jexlFilters = (0, mobx_state_tree_1.cast)(f);
+        },
         setRowHeight(arg) {
             self.rowHeightSetting = arg;
         },
@@ -97,6 +106,12 @@ function MultiVariantBaseModelF(configSchema) {
             }
             self.sourcesLoadingStopToken = str;
         },
+        setSimplifiedFeaturesLoading(str) {
+            if (self.simplifiedFeaturesStopToken) {
+                (0, stopToken_1.stopStopToken)(self.simplifiedFeaturesStopToken);
+            }
+            self.simplifiedFeaturesStopToken = str;
+        },
         setSources(sources) {
             if (!(0, fast_deep_equal_1.default)(sources, self.sourcesVolatile)) {
                 self.sourcesVolatile = sources;
@@ -122,8 +137,15 @@ function MultiVariantBaseModelF(configSchema) {
                 self.sampleInfo = arg;
             }
         },
+        setReferenceDrawingMode(arg) {
+            self.referenceDrawingMode = arg;
+        },
     }))
         .views(self => ({
+        get activeFilters() {
+            var _a;
+            return ((_a = self.jexlFilters) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'jexlFilters').map((r) => `jexl:${r}`));
+        },
         get preSources() {
             return self.layout.length ? self.layout : self.sourcesVolatile;
         },
@@ -152,6 +174,11 @@ function MultiVariantBaseModelF(configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
         return {
+            get sourceMap() {
+                return self.sources
+                    ? Object.fromEntries(self.sources.map(source => [source.name, source]))
+                    : undefined;
+            },
             get rowHeight() {
                 const { sources, autoHeight, rowHeightSetting, height } = self;
                 return autoHeight ? height / ((sources === null || sources === void 0 ? void 0 : sources.length) || 1) : rowHeightSetting;
@@ -229,6 +256,28 @@ function MultiVariantBaseModelF(configSchema) {
                             },
                         ],
                     },
+                    {
+                        label: 'Reference mode',
+                        type: 'subMenu',
+                        subMenu: [
+                            {
+                                label: 'Fill background grey, skip reference allele mouseovers (helps with large overlapping SVs)',
+                                type: 'radio',
+                                checked: self.referenceDrawingMode === 'skip',
+                                onClick: () => {
+                                    self.setReferenceDrawingMode('skip');
+                                },
+                            },
+                            {
+                                label: "Don't fill background grey, only draw actual reference alleles as grey",
+                                type: 'radio',
+                                checked: self.referenceDrawingMode === 'draw',
+                                onClick: () => {
+                                    self.setReferenceDrawingMode('draw');
+                                },
+                            },
+                        ],
+                    },
                     {
                         label: 'Filter by',
                         icon: FilterList_1.default,
@@ -245,6 +294,18 @@ function MultiVariantBaseModelF(configSchema) {
                                     ]);
                                 },
                             },
+                            {
+                                label: 'Edit filters',
+                                onClick: () => {
+                                    (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                        AddFiltersDialog,
+                                        {
+                                            model: self,
+                                            handleClose,
+                                        },
+                                    ]);
+                                },
+                            },
                         ],
                     },
                     {
@@ -278,7 +339,7 @@ function MultiVariantBaseModelF(configSchema) {
     })
         .views(self => ({
         get canDisplayLabels() {
-            return self.rowHeight > 8 && self.showSidebarLabelsSetting;
+            return self.rowHeight >= 8 && self.showSidebarLabelsSetting;
         },
         get totalHeight() {
             var _a;
@@ -298,9 +359,14 @@ function MultiVariantBaseModelF(configSchema) {
                 totalHeight: self.totalHeight,
                 renderingMode: self.renderingMode,
                 minorAlleleFrequencyFilter: self.minorAlleleFrequencyFilter,
+                lengthCutoffFilter: self.lengthCutoffFilter,
                 rowHeight: self.rowHeight,
                 sources: self.sources,
                 scrollTop: self.scrollTop,
+                referenceDrawingMode: self.referenceDrawingMode,
+                filters: new serializableFilterChain_1.default({
+                    filters: self.activeFilters,
+                }),
             };
         },
     }));

package/dist/shared/SharedVariantMixin.d.ts

@@ -193,7 +193,7 @@ export default function SharedVariantMixin(configSchema: AnyConfigurationSchemaT
 } & {
     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;

package/dist/shared/components/AddFiltersDialog.d.ts

@@ -0,0 +1,9 @@
+declare const AddFiltersDialog: ({ model, handleClose, }: {
+    model: {
+        jexlFilters?: string[];
+        activeFilters: string[];
+        setJexlFilters: (arg?: string[]) => void;
+    };
+    handleClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default AddFiltersDialog;