@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/dist/VcfFeature/index.js

@@ -1,80 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
-function dataFromVariant(variant, parser) {
-    const { REF = '', ALT, POS, CHROM, ID } = variant;
-    const start = POS - 1;
-    const [type, description] = (0, util_2.getSOTermAndDescription)(REF, ALT, parser);
-    return {
-        refName: CHROM,
-        start,
-        end: getEnd(variant),
-        description,
-        type,
-        name: ID === null || ID === void 0 ? void 0 : ID.join(','),
-    };
-}
-function getEnd(variant) {
-    var _a;
-    const { POS, REF = '', ALT = [] } = variant;
-    const isTRA = ALT.includes('<TRA>');
-    const start = POS - 1;
-    const isSymbolic = ALT.some(f => f.includes('<'));
-    if (isSymbolic) {
-        const info = variant.INFO;
-        if (info.END && !isTRA) {
-            return +info.END[0];
-        }
-        const lens = [];
-        if (info.SVLEN && !isTRA) {
-            const svlens = info.SVLEN;
-            for (let i = 0; i < svlens.length; i++) {
-                const svlen = svlens[i];
-                if ((_a = ALT[i]) === null || _a === void 0 ? void 0 : _a.startsWith('<INS')) {
-                    lens.push(1);
-                }
-                else {
-                    lens.push(Math.abs(+svlen));
-                }
-            }
-            return start + (0, util_1.max)(lens);
-        }
-    }
-    return start + REF.length;
-}
-class VCFFeature {
-    constructor(args) {
-        this.variant = args.variant;
-        this.parser = args.parser;
-        this.data = dataFromVariant(this.variant, this.parser);
-        this._id = args.id;
-    }
-    get(field) {
-        var _a;
-        return field === 'samples'
-            ? this.variant.SAMPLES()
-            : field === 'genotypes'
-                ? this.variant.GENOTYPES()
-                : ((_a = this.data[field]) !== null && _a !== void 0 ? _a : this.variant[field]);
-    }
-    parent() {
-        return undefined;
-    }
-    children() {
-        return undefined;
-    }
-    id() {
-        return this._id;
-    }
-    toJSON() {
-        const { SAMPLES, GENOTYPES, ...rest } = this.variant;
-        return {
-            uniqueId: this._id,
-            ...rest,
-            ...this.data,
-            samples: this.variant.SAMPLES(),
-        };
-    }
-}
-exports.default = VCFFeature;

package/dist/VcfFeature/util.d.ts

@@ -1,6 +0,0 @@
-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

@@ -1,227 +0,0 @@
-"use strict";
-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',
-    DUP: 'duplication',
-    INV: 'inversion',
-    INVDUP: 'inverted_duplication',
-    CNV: 'copy_number_variation',
-    TRA: 'translocation',
-    'DUP:TANDEM': 'tandem_duplication',
-    NON_REF: 'sequence_variant',
-    '*': 'sequence_variant',
-};
-function getSOTermAndDescription(ref, alt, parser) {
-    if (!alt || alt.length === 0) {
-        return ['remark', 'no alternative alleles'];
-    }
-    const soTerms = new Set();
-    let descriptions = new Set();
-    for (const a of alt) {
-        let [soTerm, description] = getSOAndDescFromAltDefs(a, parser);
-        if (!soTerm) {
-            ;
-            [soTerm, description] = getSOAndDescByExamination(ref, a);
-        }
-        if (soTerm && description) {
-            soTerms.add(soTerm);
-            descriptions.add(description);
-        }
-    }
-    if (descriptions.size > 1) {
-        const descs = [...descriptions];
-        const prefixes = new Set(descs
-            .map(desc => {
-            const prefix = desc.split('->');
-            return prefix[1] ? prefix[0] : desc;
-        })
-            .filter((f) => !!f));
-        descriptions = new Set([...prefixes]
-            .map(r => r.trim())
-            .map(prefix => {
-            const suffixes = descs
-                .map(desc => desc.split('->').map(r => r.trim()))
-                .map(pref => (pref[1] && pref[0] === prefix ? pref[1] : ''))
-                .filter(f => !!f);
-            return suffixes.length ? `${prefix} -> ${suffixes.join(',')}` : prefix;
-        }));
-    }
-    return soTerms.size
-        ? [[...soTerms].join(','), [...descriptions].join(',')]
-        : [];
-}
-function getSOAndDescFromAltDefs(alt, parser) {
-    if (typeof alt === 'string' && !alt.startsWith('<')) {
-        return [];
-    }
-    let soTerm = altTypeToSO[alt];
-    if (!soTerm && parser.getMetadata('ALT', alt)) {
-        soTerm = 'sequence_variant';
-    }
-    if (soTerm) {
-        return [soTerm, alt];
-    }
-    const modAlt = alt.split(':');
-    return modAlt.length > 1
-        ? getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser)
-        : [];
-}
-function getSOAndDescByExamination(ref, alt) {
-    const bnd = (0, vcf_1.parseBreakend)(alt);
-    if (bnd) {
-        return ['breakend', alt];
-    }
-    else if (ref.length === 1 && alt.length === 1) {
-        return ['SNV', makeDescriptionString('SNV', ref, alt)];
-    }
-    else if (alt === '<INS>') {
-        return ['insertion', alt];
-    }
-    else if (alt === '<DEL>') {
-        return ['deletion', alt];
-    }
-    else if (alt === '<DUP>') {
-        return ['duplication', alt];
-    }
-    else if (alt === '<CNV>') {
-        return ['cnv', alt];
-    }
-    else if (alt === '<INV>') {
-        return ['inversion', alt];
-    }
-    else if (alt === '<TRA>') {
-        return ['translocation', alt];
-    }
-    else if (alt.includes('<')) {
-        return ['sv', 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)];
-        }
-    }
-    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 [
-            'insertion',
-            lenRef > 5 || lenAlt > 5
-                ? `${lena} INS`
-                : makeDescriptionString('insertion', len > 5 ? lena : ref, alt),
-        ];
-    }
-    else if (ref.length > alt.length) {
-        const lenRef = ref.length;
-        const lenAlt = alt.length;
-        const lena = (0, util_1.getBpDisplayStr)(lenRef - lenAlt);
-        return [
-            'deletion',
-            lenRef > 5 || lenAlt > 5
-                ? `${lena} DEL`
-                : makeDescriptionString('deletion', 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} ${[ref, alt].join(' -> ')}`;
-}
-function makeSimpleAltString(genotype, ref, alt) {
-    return genotype
-        .split(/[/|]/)
-        .map(r => r === '.'
-        ? '.'
-        : +r === 0
-            ? `ref(${ref.length < 10 ? ref : (0, util_1.getBpDisplayStr)(ref.length)})`
-            : getMinimalDesc(ref, alt[+r - 1] || ''))
-        .join(genotype.includes('|') ? '|' : '/');
-}

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -1,25 +0,0 @@
-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;
-    protected configurePre2(): Promise<{
-        vcf: TabixIndexedFile;
-        parser: VcfParser;
-    }>;
-    configure(opts?: BaseOptions): Promise<{
-        vcf: TabixIndexedFile;
-        parser: VcfParser;
-    }>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(opts?: BaseOptions): Promise<string>;
-    getMetadata(opts?: BaseOptions): Promise<any>;
-    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    getSources(): Promise<{
-        name: string;
-    }[]>;
-}

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -1,117 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const tabix_1 = require("@gmod/tabix");
-const vcf_1 = __importDefault(require("@gmod/vcf"));
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const VcfFeature_1 = __importDefault(require("../VcfFeature"));
-class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async configurePre(_opts) {
-        const vcfGzLocation = this.getConf('vcfGzLocation');
-        const location = this.getConf(['index', 'location']);
-        const indexType = this.getConf(['index', 'indexType']);
-        const filehandle = (0, io_1.openLocation)(vcfGzLocation, this.pluginManager);
-        const isCSI = indexType === 'CSI';
-        const vcf = new tabix_1.TabixIndexedFile({
-            filehandle,
-            csiFilehandle: isCSI
-                ? (0, io_1.openLocation)(location, this.pluginManager)
-                : undefined,
-            tbiFilehandle: !isCSI
-                ? (0, io_1.openLocation)(location, this.pluginManager)
-                : undefined,
-            chunkCacheSize: 50 * 2 ** 20,
-        });
-        return {
-            vcf,
-            parser: new vcf_1.default({
-                header: await vcf.getHeader(),
-            }),
-        };
-    }
-    async configurePre2() {
-        if (!this.configured) {
-            this.configured = this.configurePre().catch((e) => {
-                this.configured = undefined;
-                throw e;
-            });
-        }
-        return this.configured;
-    }
-    async configure(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return (0, util_1.updateStatus)('Downloading index', statusCallback, () => this.configurePre2());
-    }
-    async getRefNames(opts = {}) {
-        const { vcf } = await this.configure(opts);
-        return vcf.getReferenceSequenceNames(opts);
-    }
-    async getHeader(opts) {
-        const { vcf } = await this.configure(opts);
-        return vcf.getHeader();
-    }
-    async getMetadata(opts) {
-        const { parser } = await this.configure(opts);
-        return parser.getMetadata();
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { refName, start, end } = query;
-            const { statusCallback = () => { } } = opts;
-            const { vcf, parser } = await this.configure(opts);
-            await (0, util_1.updateStatus)('Downloading variants', statusCallback, () => vcf.getLines(refName, start, end, {
-                lineCallback: (line, fileOffset) => {
-                    observer.next(new VcfFeature_1.default({
-                        variant: parser.parseLine(line),
-                        parser,
-                        id: `${this.id}-vcf-${fileOffset}`,
-                    }));
-                },
-                ...opts,
-            }));
-            observer.complete();
-        }, opts.stopToken);
-    }
-    async getSources() {
-        const conf = this.getConf('samplesTsvLocation');
-        if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
-            const { parser } = await this.configure();
-            return parser.samples.map(name => ({
-                name,
-            }));
-        }
-        else {
-            const txt = await (0, util_1.fetchAndMaybeUnzipText)((0, io_1.openLocation)(conf, this.pluginManager));
-            const lines = txt.split(/\n|\r\n|\r/);
-            const header = lines[0].split('\t');
-            const { parser } = await this.configure();
-            const metadataLines = lines
-                .slice(1)
-                .filter(f => !!f)
-                .map(line => {
-                const [name, ...rest] = line.split('\t');
-                return {
-                    ...Object.fromEntries(header.slice(1).map((c, idx) => [c, rest[idx] || ''])),
-                    name: 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));
-        }
-    }
-}
-exports.default = VcfTabixAdapter;

package/dist/VcfTabixAdapter/configSchema.d.ts

@@ -1,32 +0,0 @@
-declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    vcfGzLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        indexType: {
-            model: import("mobx-state-tree").ISimpleType<string>;
-            type: string;
-            defaultValue: string;
-        };
-        location: {
-            type: string;
-            defaultValue: {
-                uri: string;
-                locationType: string;
-            };
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    samplesTsvLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            description: string;
-            locationType: string;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default VcfTabixAdapter;

package/dist/VcfTabixAdapter/configSchema.js

@@ -1,56 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function x() { }
-const VcfTabixAdapter = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapter', {
-    vcfGzLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/my.vcf.gz',
-            locationType: 'UriLocation',
-        },
-    },
-    index: (0, configuration_1.ConfigurationSchema)('VcfIndex', {
-        indexType: {
-            model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
-            type: 'stringEnum',
-            defaultValue: 'TBI',
-        },
-        location: {
-            type: 'fileLocation',
-            defaultValue: {
-                uri: '/path/to/my.vcf.gz.tbi',
-                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,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                vcfGzLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-                index: {
-                    location: {
-                        uri: `${snap.uri}.tbi`,
-                        baseUri: snap.baseUri,
-                    },
-                },
-            }
-            : snap;
-    },
-});
-exports.default = VcfTabixAdapter;

package/dist/VcfTabixAdapter/index.d.ts

@@ -1,3 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export { default as configSchema } from './configSchema';
-export default function VcfTabixAdapterF(pluginManager: PluginManager): void;

package/dist/VcfTabixAdapter/index.js

@@ -1,52 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = void 0;
-exports.default = VcfTabixAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-var configSchema_2 = require("./configSchema");
-Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_2).default; } });
-function VcfTabixAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'VcfTabixAdapter',
-        displayName: 'VCF tabix adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfTabixAdapter'))).then(r => r.default),
-    }));
-}

package/dist/extensionPoints.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/dist/extensionPoints.js

@@ -1,39 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = ExtensionPointsF;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function ExtensionPointsF(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const fileName = (0, tracks_1.getFileName)(file);
-            const indexName = index && (0, tracks_1.getFileName)(index);
-            if ((0, util_1.testAdapter)(fileName, /\.vcf\.b?gz$/i, adapterHint, 'VcfTabixAdapter')) {
-                return {
-                    type: 'VcfTabixAdapter',
-                    vcfGzLocation: file,
-                    index: {
-                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
-                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
-                    },
-                };
-            }
-            else if ((0, util_1.testAdapter)(fileName, /\.vcf(\.gz)?$/i, adapterHint, 'VcfAdapter')) {
-                return {
-                    type: 'VcfAdapter',
-                    vcfLocation: file,
-                };
-            }
-            else {
-                return adapterGuesser(file, index, adapterHint);
-            }
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-        return (adapterName) => {
-            return ['VcfTabixAdapter', 'VcfAdapter'].includes(adapterName)
-                ? 'VariantTrack'
-                : trackTypeGuesser(adapterName);
-        };
-    });
-}