@jbrowse/plugin-variants 2.17.0 → 3.0.0

package/esm/VariantFeatureWidget/types.d.ts

@@ -0,0 +1,16 @@
+export interface Descriptions {
+    INFO?: {
+        ANN?: {
+            Description?: string;
+        };
+        CSQ?: {
+            Description?: string;
+        };
+    };
+}
+export interface ReducedFeature {
+    INFO?: {
+        ANN?: string[];
+        CSQ?: string[];
+    };
+}

package/esm/VariantFeatureWidget/types.js

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

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 +1,43 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { firstValueFrom, toArray } from 'rxjs';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util';
+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, minorAlleleFrequencyFilter, 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 = getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter);
+        for (const feat of feats) {
+            const samp = feat.get('genotypes');
+            for (const { name } of sources) {
+                const s = samp[name];
+                genotypeFactor.add(s);
+            }
+        }
+        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 +1,26 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type { SampleInfo } from '../types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export declare class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: string;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<{
+        hasPhased: boolean;
+        sampleInfo: Record<string, SampleInfo>;
+        features: {
+            id: string;
+            data: {
+                start: number;
+                end: number;
+                refName: string;
+            };
+        }[];
+    }>;
+}

package/esm/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -0,0 +1,46 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import { firstValueFrom, toArray } from 'rxjs';
+import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../util';
+export class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions {
+    constructor() {
+        super(...arguments);
+        this.name = 'MultiVariantGetSimplifiedFeatures';
+    }
+    async execute(args, rpcDriverClassName) {
+        var _a, _b;
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { minorAlleleFrequencyFilter, regions, adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
+        const feats = await firstValueFrom(dataAdapter
+            .getFeaturesInMultipleRegions(regions, deserializedArgs)
+            .pipe(toArray()));
+        const features = getFeaturesThatPassMinorAlleleFrequencyFilter(feats, minorAlleleFrequencyFilter);
+        const sampleInfo = {};
+        let hasPhased = false;
+        for (const f of features) {
+            const samp = f.get('genotypes');
+            for (const [key, val] of Object.entries(samp)) {
+                const isPhased = val.includes('|');
+                hasPhased || (hasPhased = isPhased);
+                sampleInfo[key] = {
+                    maxPloidy: Math.max(((_a = sampleInfo[key]) === null || _a === void 0 ? void 0 : _a.maxPloidy) || 0, val.split('|').length),
+                    isPhased: ((_b = sampleInfo[key]) === null || _b === void 0 ? void 0 : _b.isPhased) || isPhased,
+                };
+            }
+        }
+        return {
+            hasPhased,
+            sampleInfo,
+            features: features.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

@@ -1,11 +1,14 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
+import VcfParser from '@gmod/vcf';
+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>;
     vcfFeatures?: Promise<{
         header: string;
+        parser: VcfParser;
         intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
     }>;
     static capabilities: string[];
@@ -13,16 +16,21 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     getMetadata(): Promise<any>;
     setupP(opts?: BaseOptions): Promise<{
         header: string;
+        parser: VcfParser;
         intervalTreeMap: {
             [k: string]: (sc?: (arg: string) => void) => IntervalTree<any>;
         };
     }>;
     setup(): Promise<{
         header: string;
+        parser: VcfParser;
         intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
     }>;
     getRefNames(_?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getSources(): Promise<{
+        name: string;
+    }[]>;
     freeResources(): void;
 }
 export {};

package/esm/VcfAdapter/VcfAdapter.js

@@ -1,10 +1,9 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import IntervalTree from '@flatten-js/interval-tree';
+import VcfParser from '@gmod/vcf';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import IntervalTree from '@flatten-js/interval-tree';
-import VCF from '@gmod/vcf';
-// local
 import VcfFeature from '../VcfFeature';
 class VcfAdapter extends BaseFeatureDataAdapter {
     constructor() {
@@ -16,8 +15,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
         return header;
     }
     async getMetadata() {
-        const { header } = await this.setup();
-        const parser = new VCF({ header });
+        const { parser } = await this.setup();
         return parser.getMetadata();
     }
     async setupP(opts) {
@@ -30,8 +28,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
         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 n = buffer.indexOf(10, blockStart);
             const b = n === -1 ? buffer.subarray(blockStart) : buffer.subarray(blockStart, n);
             const line = decoder.decode(b).trim();
             if (line) {
@@ -53,7 +50,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
             blockStart = n + 1;
         }
         const header = headerLines.join('\n');
-        const parser = new VCF({ header });
+        const parser = new VcfParser({ header });
         const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
             refName,
             (sc) => {
@@ -76,6 +73,7 @@ class VcfAdapter extends BaseFeatureDataAdapter {
         ]));
         return {
             header,
+            parser,
             intervalTreeMap,
         };
     }
@@ -106,7 +104,33 @@ class VcfAdapter extends BaseFeatureDataAdapter {
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
+    }
+    async getSources() {
+        const conf = this.getConf('samplesTsvLocation');
+        if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
+            const { parser } = await this.setup();
+            return parser.samples.map(name => ({
+                name,
+            }));
+        }
+        else {
+            const txt = await openLocation(conf).readFile('utf8');
+            const lines = txt.split(/\n|\r\n|\r/);
+            const header = lines[0].split('\t');
+            const { parser } = await this.setup();
+            const s = new Set(parser.samples);
+            return lines
+                .slice(1)
+                .map(line => {
+                const cols = line.split('\t');
+                return {
+                    name: cols[0],
+                    ...Object.fromEntries(cols.slice(1).map((c, idx) => [header[idx + 1], c])),
+                };
+            })
+                .filter(f => s.has(f.name));
+        }
     }
     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: {
@@ -9,5 +6,13 @@ declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
+    samplesTsvLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            description: string;
+            locationType: string;
+        };
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default VcfAdapter;

package/esm/VcfAdapter/configSchema.js

@@ -1,15 +1,20 @@
 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' },
+        defaultValue: {
+            uri: '/path/to/my.vcf',
+            locationType: 'UriLocation',
+        },
+    },
+    samplesTsvLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/samples.tsv',
+            description: 'tsv with header like name\tpopulation\tetc. where the first column is required, and is the sample names',
+            locationType: 'UriLocation',
+        },
     },
 }, { explicitlyTyped: true });
 export default VcfAdapter;

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 +1,63 @@
-// locals
 import { getSOTermAndDescription } from './util';
+function dataFromVariant(variant, parser) {
+    const { FORMAT, 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,
+        format: FORMAT,
+    };
+}
+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
@@ -51,35 +46,27 @@ export function getSOTermAndDescription(ref, alt, parser) {
             return suffixes.length ? `${prefix} -> ${suffixes.join(',')}` : prefix;
         }));
     }
-    if (soTerms.size) {
-        return [[...soTerms].join(','), [...descriptions].join(',')];
-    }
-    return [];
+    return soTerms.size
+        ? [[...soTerms].join(','), [...descriptions].join(',')]
+        : [];
 }
 export function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {
         return [];
     }
-    // look for a definition with an SO type for this
     let soTerm = altTypeToSO[alt];
-    // if no SO term but ALT is in metadata, assume sequence_variant
     if (!soTerm && parser.getMetadata('ALT', alt)) {
         soTerm = 'sequence_variant';
     }
     if (soTerm) {
         return [soTerm, alt];
     }
-    // try to look for a definition for a parent term if we can
     const modAlt = alt.split(':');
     if (modAlt.length > 1) {
         return getSOAndDescFromAltDefs(`<${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) {

package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -1,8 +1,9 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { NoAssemblyRegion } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 import VcfParser from '@gmod/vcf';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
 export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     private configured?;
     private configurePre;
@@ -14,5 +15,8 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     getHeader(): Promise<string>;
     getMetadata(): Promise<any>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getSources(): Promise<{
+        name: string;
+    }[]>;
     freeResources(): void;
 }