@jbrowse/plugin-variants 2.16.1 → 2.18.0

package/esm/VariantFeatureWidget/VariantFeatureWidget.js

@@ -1,13 +1,11 @@
-import React, { lazy, Suspense } from 'react';
-import { observer } from 'mobx-react';
-import { Paper } from '@mui/material';
-import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
+import React, { Suspense, lazy } from 'react';
 import { parseBreakend } from '@gmod/vcf';
-// locals
-import VariantSampleGrid from './VariantSampleGrid';
+import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
+import { Paper } from '@mui/material';
+import { observer } from 'mobx-react';
 import VariantAnnotationTable from './VariantAnnotationTable';
+import VariantSampleGrid from './VariantSampleGrid';
 import { variantFieldDescriptions } from './variantFieldDescriptions';
-// lazies
 const LaunchBreakendPanel = lazy(() => import('./LaunchBreakendPanel'));
 function AnnPanel({ descriptions, feature, }) {
     var _a, _b, _c, _d, _e;

package/esm/VariantFeatureWidget/VariantSampleGrid.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function VariantSamples(props: {
     feature: SimpleFeatureSerialized;
     descriptions?: {

package/esm/VariantFeatureWidget/VariantSampleGrid.js

@@ -1,8 +1,8 @@
 import React, { useState } from 'react';
-import { FormControlLabel, Checkbox, TextField, Typography, } from '@mui/material';
-import { DataGrid, GridToolbar } from '@mui/x-data-grid';
-import { measureGridWidth } from '@jbrowse/core/util';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
+import { measureGridWidth } from '@jbrowse/core/util';
+import { Checkbox, FormControlLabel, TextField, Typography, } from '@mui/material';
+import { DataGrid, GridToolbar } from '@mui/x-data-grid';
 function SampleFilters({ columns, filter, setFilter, }) {
     return (React.createElement(React.Fragment, null,
         React.createElement(Typography, null, "These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),
@@ -19,9 +19,6 @@ export default function VariantSamples(props) {
     let error;
     let rows = [];
     const filters = Object.keys(filter);
-    // catch some error thrown from regex
-    // note: maps all values into a string, if this is not done rows are not
-    // sortable by the data-grid
     try {
         rows = preFilteredRows
             .map(row => {
@@ -54,19 +51,18 @@ export default function VariantSamples(props) {
             width: widths[index],
         });
     });
-    // disableRowSelectionOnClick helps avoid
-    // https://github.com/mui-org/material-ui-x/issues/1197
     return !preFilteredRows.length ? null : (React.createElement(BaseCard, { ...props, title: "Samples" },
         error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
         React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: checked, onChange: event => {
                     setChecked(event.target.checked);
                 } }), label: React.createElement(Typography, { variant: "body2" }, "Show options") }),
         checked ? (React.createElement(SampleFilters, { setFilter: setFilter, columns: columns, filter: filter })) : null,
-        React.createElement(DataGrid, { autoHeight: true, rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? GridToolbar : null }, slotProps: {
-                toolbar: {
-                    printOptions: {
-                        disableToolbarButton: true,
+        React.createElement("div", { style: { display: 'flex', flexDirection: 'column' } },
+            React.createElement(DataGrid, { rows: rows, hideFooter: rows.length < 100, columns: columns, disableRowSelectionOnClick: true, rowHeight: 25, columnHeaderHeight: 35, disableColumnMenu: true, slots: { toolbar: checked ? GridToolbar : null }, slotProps: {
+                    toolbar: {
+                        printOptions: {
+                            disableToolbarButton: true,
+                        },
                     },
-                },
-            } })));
+                } }))));
 }

package/esm/VariantFeatureWidget/index.d.ts

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

package/esm/VariantFeatureWidget/index.js

@@ -1,7 +1,7 @@
 import { lazy } from 'react';
 import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
-import { stateModelFactory } from './stateModelFactory';
 import { configSchema } from './configSchema';
+import { stateModelFactory } from './stateModelFactory';
 export default function VariantFeatureWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType({
         name: 'VariantFeatureWidget',

package/esm/VariantFeatureWidget/stateModelFactory.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { Instance } from 'mobx-state-tree';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
@@ -93,8 +93,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: string | undefined;
     trackType: string | undefined;
     maxDepth: number | undefined;
-    formattedFields: any;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
+    formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/VariantFeatureWidget/stateModelFactory.js

@@ -1,5 +1,5 @@
-import { types } from 'mobx-state-tree';
 import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
+import { types } from 'mobx-state-tree';
 export function stateModelFactory(pluginManager) {
     const baseModel = baseModelFactory(pluginManager);
     return types.compose(baseModel, types.model('VariantFeatureWidget', {

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.d.ts

@@ -0,0 +1,17 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export declare class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: string;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<Record<string, {
+        name: string;
+        genotypes: number[];
+    }>>;
+}

package/esm/VariantRPC/MultiVariantGetGenotypeMatrix.js

@@ -0,0 +1,60 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { firstValueFrom, toArray } from 'rxjs';
+export class MultiVariantGetGenotypeMatrix extends RpcMethodTypeWithFiltersAndRenameRegions {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiVariantGetGenotypeMatrix';
+    }
+    async execute(args, rpcDriverClassName) {
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { sources, mafFilter, regions, adapterConfig, sessionId } = deserializedArgs;
+        const adapter = await getAdapter(pm, sessionId, adapterConfig);
+        const dataAdapter = adapter.dataAdapter;
+        const region = regions[0];
+        const feats = await firstValueFrom(dataAdapter.getFeatures(region, deserializedArgs).pipe(toArray()));
+        const genotypeFactor = new Set();
+        const mafs = [];
+        for (const feat of feats) {
+            let c = 0;
+            let c2 = 0;
+            const samp = feat.get('genotypes');
+            if (feat.get('end') - feat.get('start') <= 10) {
+                for (const { name } of sources) {
+                    const s = samp[name];
+                    genotypeFactor.add(s);
+                    if (s === '0|0' || s === './.') {
+                        c2++;
+                    }
+                    else if (s === '1|0' || s === '0|1') {
+                        c++;
+                    }
+                    else if (s === '1|1') {
+                        c++;
+                        c2++;
+                    }
+                    else {
+                        c++;
+                    }
+                }
+                if (c / sources.length > mafFilter &&
+                    c2 / sources.length < 1 - mafFilter) {
+                    mafs.push(feat);
+                }
+            }
+        }
+        const genotypeFactorMap = Object.fromEntries([...genotypeFactor].map((type, idx) => [type, idx]));
+        const rows = {};
+        for (const feat of mafs) {
+            const samp = feat.get('genotypes');
+            for (const { name } of sources) {
+                if (!rows[name]) {
+                    rows[name] = { name, genotypes: [] };
+                }
+                rows[name].genotypes.push(genotypeFactorMap[samp[name]]);
+            }
+        }
+        return rows;
+    }
+}

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.d.ts

@@ -0,0 +1,21 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+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<{
+        id: string;
+        data: {
+            start: number;
+            end: number;
+            refName: string;
+        };
+    }[]>;
+}

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -0,0 +1,56 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { firstValueFrom, toArray } from 'rxjs';
+export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiVariantGetSimplifiedFeatures';
+    }
+    async execute(args, rpcDriverClassName) {
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { mafFilter, sources, regions, adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
+        const feats = await firstValueFrom(dataAdapter
+            .getFeaturesInMultipleRegions(regions, deserializedArgs)
+            .pipe(toArray()));
+        const genotypeFactor = new Set();
+        const mafs = [];
+        for (const feat of feats) {
+            let c = 0;
+            let c2 = 0;
+            const samp = feat.get('genotypes');
+            if (feat.get('end') - feat.get('start') <= 10) {
+                for (const { name } of sources) {
+                    const s = samp[name];
+                    genotypeFactor.add(s);
+                    if (s === '0|0' || s === './.') {
+                        c2++;
+                    }
+                    else if (s === '1|0' || s === '0|1') {
+                        c++;
+                    }
+                    else if (s === '1|1') {
+                        c++;
+                        c2++;
+                    }
+                    else {
+                        c++;
+                    }
+                }
+                if (c / sources.length > mafFilter &&
+                    c2 / sources.length < 1 - mafFilter) {
+                    mafs.push(feat);
+                }
+            }
+        }
+        return mafs.map(f => ({
+            id: f.id(),
+            data: {
+                start: f.get('start'),
+                end: f.get('end'),
+                refName: f.get('refName'),
+            },
+        }));
+    }
+}

package/esm/VariantRPC/MultiVariantGetSources.d.ts

@@ -0,0 +1,14 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export declare class MultiVariantGetSources extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: string;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<any>;
+}

package/esm/VariantRPC/MultiVariantGetSources.js

@@ -0,0 +1,15 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+export class MultiVariantGetSources extends RpcMethodTypeWithFiltersAndRenameRegions {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiVariantGetSources';
+    }
+    async execute(args, rpcDriverClassName) {
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { regions, adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
+        return dataAdapter.getSources(regions, deserializedArgs);
+    }
+}

package/esm/VariantTrack/configSchema.d.ts

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

package/esm/VariantTrack/configSchema.js

@@ -1,15 +1,7 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
-/**
- * #config VariantTrack
- * Mostly similar to feature track, but has `ChordDisplayType` registered to it,
- * and custom feature details in `LinearVariantDisplay`
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const configSchema = (pluginManager) => ConfigurationSchema('VariantTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
-    baseConfiguration: createBaseTrackConfig(pluginManager),
-});
-export default configSchema;
+export default function VariantTrackF(pluginManager) {
+    return ConfigurationSchema('VariantTrack', {}, {
+        baseConfiguration: createBaseTrackConfig(pluginManager),
+    });
+}

package/esm/VariantTrack/index.d.ts

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

package/esm/VcfAdapter/VcfAdapter.d.ts

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

package/esm/VcfAdapter/VcfAdapter.js

@@ -1,11 +1,9 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { updateStatus, isGzip } from '@jbrowse/core/util';
-import { openLocation } from '@jbrowse/core/util/io';
-import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import IntervalTree from '@flatten-js/interval-tree';
-import { unzip } from '@gmod/bgzf-filehandle';
 import VCF from '@gmod/vcf';
-// local
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import VcfFeature from '../VcfFeature';
 class VcfAdapter extends BaseFeatureDataAdapter {
     constructor() {
@@ -23,20 +21,17 @@ class VcfAdapter extends BaseFeatureDataAdapter {
     }
     async setupP(opts) {
         const { statusCallback = () => { } } = opts || {};
-        const buf = (await openLocation(this.getConf('vcfLocation'), this.pluginManager).readFile(opts));
-        const buffer = isGzip(buf)
-            ? await updateStatus('Unzipping', statusCallback, () => unzip(buf))
-            : buf;
+        const loc = openLocation(this.getConf('vcfLocation'), this.pluginManager);
+        const buffer = await fetchAndMaybeUnzip(loc, opts);
         const headerLines = [];
         const featureMap = {};
         let blockStart = 0;
-        const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+        const decoder = new TextDecoder('utf8');
         let i = 0;
         while (blockStart < buffer.length) {
             const n = buffer.indexOf('\n', blockStart);
-            // could be a non-newline ended file, so slice to end of file if n===-1
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
-            const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+            const line = decoder.decode(b).trim();
             if (line) {
                 if (line.startsWith('#')) {
                     headerLines.push(line);
@@ -109,7 +104,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/esm/VcfAdapter/configSchema.d.ts

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

package/esm/VcfAdapter/configSchema.js

@@ -1,12 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config VcfAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const VcfAdapter = ConfigurationSchema('VcfAdapter', {
-    /**
-     * #slot
-     */
     vcfLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },

package/esm/VcfAdapter/index.d.ts

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

package/esm/VcfFeature/index.d.ts

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

package/esm/VcfFeature/index.js

@@ -1,53 +1,62 @@
-// locals
 import { getSOTermAndDescription } from './util';
+function dataFromVariant(variant, parser) {
+    const { REF = '', ALT, POS, CHROM, ID } = variant;
+    const start = POS - 1;
+    const [type, description] = getSOTermAndDescription(REF, ALT, parser);
+    return {
+        refName: CHROM,
+        start,
+        end: getEnd(variant),
+        description,
+        type,
+        name: ID === null || ID === void 0 ? void 0 : ID.join(','),
+        aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
+    };
+}
+function getEnd(variant) {
+    const { POS, REF = '', ALT } = variant;
+    const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.includes('<TRA>');
+    const start = POS - 1;
+    const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
+    if (isSymbolic) {
+        const info = variant.INFO;
+        if (info.END && !isTRA) {
+            return +info.END[0];
+        }
+    }
+    return start + REF.length;
+}
 export default class VCFFeature {
     constructor(args) {
         this.variant = args.variant;
         this.parser = args.parser;
-        this.data = this.dataFromVariant(this.variant);
+        this.data = dataFromVariant(this.variant, this.parser);
         this._id = args.id;
     }
     get(field) {
         var _a;
         return field === 'samples'
-            ? this.variant.SAMPLES
-            : ((_a = this.data[field]) !== null && _a !== void 0 ? _a : this.variant[field]);
+            ? this.variant.SAMPLES()
+            : field === 'genotypes'
+                ? this.variant.GENOTYPES()
+                : ((_a = this.data[field]) !== null && _a !== void 0 ? _a : this.variant[field]);
     }
-    set() { }
     parent() {
         return undefined;
     }
     children() {
         return undefined;
     }
-    tags() {
-        return [...Object.keys(this.data), ...Object.keys(this.variant), 'samples'];
-    }
     id() {
         return this._id;
     }
-    dataFromVariant(variant) {
-        const { REF, ALT, POS, CHROM, INFO, ID } = variant;
-        const start = POS - 1;
-        const [type, description] = getSOTermAndDescription(REF, ALT, this.parser);
-        const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.includes('<TRA>');
-        const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
-        return {
-            refName: CHROM,
-            start,
-            end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,
-            description,
-            type,
-            name: ID === null || ID === void 0 ? void 0 : ID.join(','),
-            aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
-        };
-    }
     toJSON() {
+        const { SAMPLES, GENOTYPES, ...rest } = this.variant;
         return {
             uniqueId: this._id,
-            ...this.variant,
+            ...rest,
             ...this.data,
-            samples: this.variant.SAMPLES,
+            samples: this.variant.SAMPLES(),
         };
     }
 }

package/esm/VcfFeature/util.d.ts

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

package/esm/VcfFeature/util.js

@@ -11,11 +11,7 @@ const altTypeToSO = {
     NON_REF: 'sequence_variant',
     '*': 'sequence_variant',
 };
-/**
- * Get a sequence ontology (SO) term that describes the variant type
- */
 export function getSOTermAndDescription(ref, alt, parser) {
-    // it's just a remark if there are no alternate alleles
     if (!alt || alt.length === 0) {
         return ['remark', 'no alternative alleles'];
     }
@@ -32,7 +28,6 @@ export function getSOTermAndDescription(ref, alt, parser) {
             descriptions.add(description);
         }
     });
-    // Combine descriptions like ["SNV G -> A", "SNV G -> T"] to ["SNV G -> A,T"]
     if (descriptions.size > 1) {
         const descs = [...descriptions];
         const prefixes = new Set(descs
@@ -60,26 +55,19 @@ export function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {
         return [];
     }
-    // look for a definition with an SO type for this
     let soTerm = altTypeToSO[alt];
-    // if no SO term but ALT is in metadata, assume sequence_variant
     if (!soTerm && parser.getMetadata('ALT', alt)) {
         soTerm = 'sequence_variant';
     }
     if (soTerm) {
         return [soTerm, alt];
     }
-    // try to look for a definition for a parent term if we can
     const modAlt = alt.split(':');
     if (modAlt.length > 1) {
         return getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser);
     }
-    // no parent
     return [];
 }
-// note: term SNV is used instead of SNP because SO definition of SNP says
-// abundance must be at least 1% in population, and can't be sure we meet
-// that
 export function getSOAndDescByExamination(ref, alt) {
     const bnd = parseBreakend(alt);
     if (bnd) {