@jbrowse/plugin-variants 3.1.0 → 3.3.0

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',
@@ -22,7 +25,7 @@ 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) {
             ;
@@ -32,7 +35,7 @@ function getSOTermAndDescription(ref, alt, parser) {
             soTerms.add(soTerm);
             descriptions.add(description);
         }
-    });
+    }
     if (descriptions.size > 1) {
         const descs = [...descriptions];
         const prefixes = new Set(descs
@@ -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.js

@@ -90,17 +90,27 @@ 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);
-            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):`, (0, util_1.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):`, (0, util_1.shorten2)(vcfSamplesNotInMetadata.map(m => m).join(',')));
+            }
+            return metadataLines.filter(f => vcfSampleSet.has(f.name));
         }
     }
     freeResources() { }

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/index.js

@@ -14,6 +14,7 @@ const MultiLinearVariantRenderer_1 = __importDefault(require("./MultiLinearVaria
 const SplitVcfTabixAdapter_1 = __importDefault(require("./SplitVcfTabixAdapter"));
 const StructuralVariantChordRenderer_1 = __importDefault(require("./StructuralVariantChordRenderer"));
 const VariantFeatureWidget_1 = __importDefault(require("./VariantFeatureWidget"));
+const MultiVariantClusterGenotypeMatrix_1 = require("./VariantRPC/MultiVariantClusterGenotypeMatrix");
 const MultiVariantGetGenotypeMatrix_1 = require("./VariantRPC/MultiVariantGetGenotypeMatrix");
 const MultiVariantGetSimplifiedFeatures_1 = require("./VariantRPC/MultiVariantGetSimplifiedFeatures");
 const MultiVariantGetSources_1 = require("./VariantRPC/MultiVariantGetSources");
@@ -42,6 +43,7 @@ class VariantsPlugin extends Plugin_1.default {
         (0, ChordVariantDisplay_1.default)(pluginManager);
         pluginManager.addRpcMethod(() => new MultiVariantGetSources_1.MultiVariantGetSources(pluginManager));
         pluginManager.addRpcMethod(() => new MultiVariantGetGenotypeMatrix_1.MultiVariantGetGenotypeMatrix(pluginManager));
+        pluginManager.addRpcMethod(() => new MultiVariantClusterGenotypeMatrix_1.MultiVariantClusterGenotypeMatrix(pluginManager));
         pluginManager.addRpcMethod(() => new MultiVariantGetSimplifiedFeatures_1.MultiVariantGetSimplifiedFeatures(pluginManager));
     }
 }

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;
@@ -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;
@@ -253,8 +265,19 @@ 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;
+        id: string;
+        baseUri?: string;
+        name: string;
+        color?: string;
+        group?: string;
+        HP?: number;
+    }[] | undefined;
     readonly sources: {
         label: string;
         id: string;
@@ -265,6 +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 | {
@@ -318,6 +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">> & {
@@ -330,10 +376,20 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
         type?: undefined;
         checked?: undefined;
         onClick?: undefined;
+    } | {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+        type?: undefined;
+        checked?: undefined;
+        subMenu?: undefined;
     })[];
 } & {
     readonly canDisplayLabels: boolean;
     readonly totalHeight: number;
+    readonly featuresReady: boolean;
 } & {
     renderProps(): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;