@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/dist/VariantRPC/MultiVariantGetSimplifiedFeatures.js

@@ -1,58 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.MultiVariantGetSimplifiedFeatures = void 0;
-const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
-const util_1 = require("@jbrowse/core/util");
-const rxjs_1 = require("rxjs");
-const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
-class MultiVariantGetSimplifiedFeatures extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'MultiVariantGetSimplifiedFeatures';
-    }
-    async execute(args, rpcDriverClassName) {
-        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { lengthCutoffFilter, minorAlleleFrequencyFilter, regions, adapterConfig, stopToken, sessionId, } = deserializedArgs;
-        const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig);
-        const features = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
-            minorAlleleFrequencyFilter,
-            lengthCutoffFilter,
-            stopToken,
-            features: await (0, rxjs_1.firstValueFrom)(dataAdapter
-                .getFeaturesInMultipleRegions(regions, deserializedArgs)
-                .pipe((0, rxjs_1.toArray)())),
-        });
-        const sampleInfo = {};
-        let hasPhased = false;
-        (0, util_1.forEachWithStopTokenCheck)(features, stopToken, ({ feature }) => {
-            var _a, _b;
-            const samp = feature.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(({ feature }) => ({
-                id: feature.id(),
-                data: {
-                    start: feature.get('start'),
-                    end: feature.get('end'),
-                    refName: feature.get('refName'),
-                    name: feature.get('name'),
-                },
-            })),
-        };
-    }
-}
-exports.MultiVariantGetSimplifiedFeatures = MultiVariantGetSimplifiedFeatures;

package/dist/VariantRPC/MultiVariantGetSources.d.ts

@@ -1,14 +0,0 @@
-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/dist/VariantRPC/MultiVariantGetSources.js

@@ -1,22 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.MultiVariantGetSources = void 0;
-const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-const RpcMethodTypeWithFiltersAndRenameRegions_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions"));
-class MultiVariantGetSources extends RpcMethodTypeWithFiltersAndRenameRegions_1.default {
-    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 (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig);
-        return dataAdapter.getSources(regions, deserializedArgs);
-    }
-}
-exports.MultiVariantGetSources = MultiVariantGetSources;

package/dist/VariantRPC/getGenotypeMatrix.d.ts

@@ -1,6 +0,0 @@
-import type { GetGenotypeMatrixArgs } from './types';
-import type PluginManager from '@jbrowse/core/PluginManager';
-export declare function getGenotypeMatrix({ pluginManager, args, }: {
-    pluginManager: PluginManager;
-    args: GetGenotypeMatrixArgs;
-}): Promise<Record<string, number[]>>;

package/dist/VariantRPC/getGenotypeMatrix.js

@@ -1,68 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getGenotypeMatrix = getGenotypeMatrix;
-const dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
-const util_1 = require("@jbrowse/core/util");
-const rxjs_1 = require("rxjs");
-const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils");
-async function getGenotypeMatrix({ pluginManager, args, }) {
-    const { sources, minorAlleleFrequencyFilter, regions, adapterConfig, sessionId, lengthCutoffFilter, stopToken, } = args;
-    const adapter = await (0, dataAdapterCache_1.getAdapter)(pluginManager, sessionId, adapterConfig);
-    const dataAdapter = adapter.dataAdapter;
-    const genotypeFactor = new Set();
-    const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
-        minorAlleleFrequencyFilter,
-        lengthCutoffFilter,
-        stopToken,
-        features: await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe((0, rxjs_1.toArray)())),
-    });
-    for (const { alleleCounts } of mafs) {
-        for (const alt of Object.keys(alleleCounts)) {
-            genotypeFactor.add(alt);
-        }
-    }
-    const rows = {};
-    const cacheSplit = {};
-    (0, util_1.forEachWithStopTokenCheck)(mafs, stopToken, ({ feature }) => {
-        const genotypes = feature.get('genotypes');
-        for (const { name } of sources) {
-            if (!rows[name]) {
-                rows[name] = [];
-            }
-            const val = genotypes[name];
-            let alleles;
-            if (cacheSplit[val]) {
-                alleles = cacheSplit[val];
-            }
-            else {
-                alleles = val.split(/[/|]/);
-                cacheSplit[val] = alleles;
-            }
-            let genotypeStatus = 0;
-            let nonRefCount = 0;
-            let uncalledCount = 0;
-            for (const l of alleles) {
-                if (l === '.') {
-                    uncalledCount++;
-                }
-                else if (l !== '0') {
-                    nonRefCount++;
-                }
-            }
-            if (uncalledCount === alleles.length) {
-                genotypeStatus = -1;
-            }
-            else if (nonRefCount === 0) {
-                genotypeStatus = 0;
-            }
-            else if (nonRefCount === alleles.length) {
-                genotypeStatus = 2;
-            }
-            else {
-                genotypeStatus = 1;
-            }
-            rows[name].push(genotypeStatus);
-        }
-    });
-    return rows;
-}

package/dist/VariantRPC/types.d.ts

@@ -1,36 +0,0 @@
-import type { Source } from '../shared/types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Region } from '@jbrowse/core/util';
-export interface GetGenotypeMatrixArgs {
-    sources: Source[];
-    minorAlleleFrequencyFilter: number;
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
-    lengthCutoffFilter: number;
-}
-export interface GetSimplifiedFeaturesArgs {
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
-    minorAlleleFrequencyFilter: number;
-    lengthCutoffFilter: number;
-}
-export interface ClusterGenotypeMatrixArgs {
-    adapterConfig: AnyConfigurationModel;
-    stopToken?: string;
-    statusCallback: (arg: string) => void;
-    sessionId: string;
-    headers?: Record<string, string>;
-    regions: Region[];
-    bpPerPx: number;
-    sources: Source[];
-    minorAlleleFrequencyFilter: number;
-    lengthCutoffFilter: number;
-}

package/dist/VariantRPC/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/VariantTrack/configSchema.d.ts

@@ -1,79 +0,0 @@
-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;
-        defaultValue: string;
-    };
-    assemblyNames: {
-        description: string;
-        type: string;
-        defaultValue: string[];
-    };
-    description: {
-        description: string;
-        type: string;
-        defaultValue: string;
-    };
-    category: {
-        description: string;
-        type: string;
-        defaultValue: never[];
-    };
-    metadata: {
-        type: string;
-        description: string;
-        defaultValue: {};
-    };
-    adapter: import("mobx-state-tree").IAnyModelType;
-    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        indexingAttributes: {
-            type: string;
-            description: string;
-            defaultValue: string[];
-        };
-        indexingFeatureTypesToExclude: {
-            type: string;
-            description: string;
-            defaultValue: string[];
-        };
-        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
-    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        feature: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        subfeatures: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        depth: {
-            type: string;
-            defaultValue: number;
-            description: string;
-        };
-        maxDepth: {
-            type: string;
-            defaultValue: number;
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        config: {
-            type: string;
-            description: string;
-            defaultValue: {};
-            contextVariable: string[];
-        };
-        hideUris: {
-            type: string;
-            defaultValue: boolean;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;

package/dist/VariantTrack/configSchema.js

@@ -1,10 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = VariantTrackF;
-const configuration_1 = require("@jbrowse/core/configuration");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-function VariantTrackF(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('VariantTrack', {}, {
-        baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
-    });
-}

package/dist/VariantTrack/index.d.ts

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

package/dist/VariantTrack/index.js

@@ -1,20 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = VariantTrackF;
-const TrackType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TrackType"));
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-const configSchema_1 = __importDefault(require("./configSchema"));
-function VariantTrackF(pm) {
-    pm.addTrackType(() => {
-        const configSchema = (0, configSchema_1.default)(pm);
-        return new TrackType_1.default({
-            name: 'VariantTrack',
-            displayName: 'Variant track',
-            configSchema,
-            stateModel: (0, models_1.createBaseTrackModel)(pm, 'VariantTrack', configSchema),
-        });
-    });
-}

package/dist/VcfAdapter/VcfAdapter.d.ts

@@ -1,35 +0,0 @@
-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<Feature>>;
-    vcfFeatures?: Promise<{
-        header: string;
-        parser: VcfParser;
-        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree<Feature>>;
-    }>;
-    static capabilities: string[];
-    getHeader(): Promise<string>;
-    getMetadata(): Promise<any>;
-    setupP(opts?: BaseOptions): Promise<{
-        header: string;
-        parser: VcfParser;
-        intervalTreeMap: {
-            [k: string]: (sc?: (arg: string) => void) => IntervalTree<Feature>;
-        };
-    }>;
-    setup(): Promise<{
-        header: string;
-        parser: VcfParser;
-        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree<Feature>>;
-    }>;
-    getRefNames(_?: BaseOptions): Promise<string[]>;
-    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    getSources(): Promise<{
-        name: string;
-    }[]>;
-}
-export {};

package/dist/VcfAdapter/VcfAdapter.js

@@ -1,119 +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 interval_tree_1 = require("@flatten-js/interval-tree");
-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"));
-const vcfParser_1 = require("./vcfParser");
-class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.calculatedIntervalTreeMap = {};
-    }
-    async getHeader() {
-        const { header } = await this.setup();
-        return header;
-    }
-    async getMetadata() {
-        const { parser } = await this.setup();
-        return parser.getMetadata();
-    }
-    async setupP(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        const loc = (0, io_1.openLocation)(this.getConf('vcfLocation'), this.pluginManager);
-        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
-        const { header, featureMap } = (0, vcfParser_1.parseVcfBuffer)(buffer, statusCallback);
-        const parser = new vcf_1.default({ header });
-        const intervalTreeMap = Object.fromEntries(Object.entries(featureMap).map(([refName, lines]) => [
-            refName,
-            (sc) => {
-                if (!this.calculatedIntervalTreeMap[refName]) {
-                    sc === null || sc === void 0 ? void 0 : sc('Parsing VCF data');
-                    let idx = 0;
-                    const intervalTree = new interval_tree_1.IntervalTree();
-                    for (const line of lines) {
-                        const f = new VcfFeature_1.default({
-                            variant: parser.parseLine(line),
-                            parser,
-                            id: `${this.id}-${refName}-${idx++}`,
-                        });
-                        intervalTree.insert([f.get('start'), f.get('end')], f);
-                    }
-                    this.calculatedIntervalTreeMap[refName] = intervalTree;
-                }
-                return this.calculatedIntervalTreeMap[refName];
-            },
-        ]));
-        return {
-            header,
-            parser,
-            intervalTreeMap,
-        };
-    }
-    async setup() {
-        if (!this.vcfFeatures) {
-            this.vcfFeatures = this.setupP().catch((e) => {
-                this.vcfFeatures = undefined;
-                throw e;
-            });
-        }
-        return this.vcfFeatures;
-    }
-    async getRefNames(_ = {}) {
-        const { intervalTreeMap } = await this.setup();
-        return Object.keys(intervalTreeMap);
-    }
-    getFeatures(region, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            var _a;
-            try {
-                const { start, end, refName } = region;
-                const { intervalTreeMap } = await this.setup();
-                for (const f of ((_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
-                    start,
-                    end,
-                ])) || []) {
-                    observer.next(f);
-                }
-                observer.complete();
-            }
-            catch (e) {
-                observer.error(e);
-            }
-        }, 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 (0, io_1.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));
-        }
-    }
-}
-VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
-exports.default = VcfAdapter;

package/dist/VcfAdapter/configSchema.d.ts

@@ -1,18 +0,0 @@
-declare const VcfAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    vcfLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    samplesTsvLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            description: string;
-            locationType: string;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default VcfAdapter;

package/dist/VcfAdapter/configSchema.js

@@ -1,35 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const VcfAdapter = (0, configuration_1.ConfigurationSchema)('VcfAdapter', {
-    vcfLocation: {
-        type: 'fileLocation',
-        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,
-    preProcessSnapshot: snap => {
-        return snap.uri
-            ? {
-                ...snap,
-                vcfLocation: {
-                    uri: snap.uri,
-                    baseUri: snap.baseUri,
-                },
-            }
-            : snap;
-    },
-});
-exports.default = VcfAdapter;

package/dist/VcfAdapter/index.d.ts

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

package/dist/VcfAdapter/index.js

@@ -1,49 +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.default = VcfAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function VcfAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'VcfAdapter',
-        displayName: 'VCF adapter',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./VcfAdapter'))).then(r => r.default),
-    }));
-}

package/dist/VcfAdapter/vcfParser.d.ts

@@ -1,7 +0,0 @@
-import type { StatusCallback } from '@jbrowse/core/util/parseLineByLine';
-interface VcfParseResult {
-    header: string;
-    featureMap: Record<string, string[]>;
-}
-export declare function parseVcfBuffer(buffer: Uint8Array, statusCallback?: StatusCallback): VcfParseResult;
-export {};

package/dist/VcfAdapter/vcfParser.js

@@ -1,26 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseVcfBuffer = parseVcfBuffer;
-const parseLineByLine_1 = require("@jbrowse/core/util/parseLineByLine");
-function parseVcfBuffer(buffer, statusCallback = () => { }) {
-    const headerLines = [];
-    const featureMap = {};
-    (0, parseLineByLine_1.parseLineByLine)(buffer, line => {
-        if (line.startsWith('#')) {
-            headerLines.push(line);
-        }
-        else {
-            const ret = line.indexOf('\t');
-            const refName = line.slice(0, ret);
-            if (!featureMap[refName]) {
-                featureMap[refName] = [];
-            }
-            featureMap[refName].push(line);
-        }
-        return true;
-    }, statusCallback);
-    return {
-        header: headerLines.join('\n'),
-        featureMap,
-    };
-}

package/dist/VcfFeature/index.d.ts

@@ -1,19 +0,0 @@
-import { type Feature } from '@jbrowse/core/util';
-import type VCFParser from '@gmod/vcf';
-import type { Variant } from '@gmod/vcf';
-export default class VCFFeature implements Feature {
-    private variant;
-    private parser;
-    private data;
-    private _id;
-    constructor(args: {
-        variant: Variant;
-        parser: VCFParser;
-        id: string;
-    });
-    get(field: string): any;
-    parent(): undefined;
-    children(): undefined;
-    id(): string;
-    toJSON(): any;
-}