@jbrowse/plugin-variants 2.17.0 → 3.0.0

package/dist/VariantTrack/configSchema.js

@@ -1,17 +1,10 @@
 "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");
-/**
- * #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) => (0, configuration_1.ConfigurationSchema)('VariantTrack', {}, {
-    /**
-     * #baseConfiguration
-     */
-    baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
-});
-exports.default = configSchema;
+function VariantTrackF(pluginManager) {
+    return (0, configuration_1.ConfigurationSchema)('VariantTrack', {}, {
+        baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
+    });
+}

package/dist/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/dist/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/dist/VcfAdapter/VcfAdapter.js

@@ -3,13 +3,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const interval_tree_1 = __importDefault(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 interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-const vcf_1 = __importDefault(require("@gmod/vcf"));
-// local
 const VcfFeature_1 = __importDefault(require("../VcfFeature"));
 class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor() {
@@ -21,8 +20,7 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         return header;
     }
     async getMetadata() {
-        const { header } = await this.setup();
-        const parser = new vcf_1.default({ header });
+        const { parser } = await this.setup();
         return parser.getMetadata();
     }
     async setupP(opts) {
@@ -35,8 +33,7 @@ class VcfAdapter extends BaseAdapter_1.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) {
@@ -81,6 +78,7 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         ]));
         return {
             header,
+            parser,
             intervalTreeMap,
         };
     }
@@ -111,7 +109,33 @@ class VcfAdapter extends BaseAdapter_1.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 (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));
+        }
     }
     freeResources() { }
 }

package/dist/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/dist/VcfAdapter/configSchema.js

@@ -1,17 +1,22 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config VcfAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const VcfAdapter = (0, configuration_1.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 });
 exports.default = VcfAdapter;

package/dist/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/dist/VcfAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+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 };
 };

package/dist/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/dist/VcfFeature/index.js

@@ -1,55 +1,65 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-// locals
 const util_1 = require("./util");
+function dataFromVariant(variant, parser) {
+    const { FORMAT, REF = '', ALT, POS, CHROM, ID } = variant;
+    const start = POS - 1;
+    const [type, description] = (0, util_1.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;
+}
 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] = (0, util_1.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/dist/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/dist/VcfFeature/util.js

@@ -16,11 +16,7 @@ const altTypeToSO = {
     NON_REF: 'sequence_variant',
     '*': 'sequence_variant',
 };
-/**
- * Get a sequence ontology (SO) term that describes the variant type
- */
 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'];
     }
@@ -37,7 +33,6 @@ 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
@@ -56,35 +51,27 @@ function getSOTermAndDescription(ref, alt, parser) {
             return suffixes.length ? `${prefix} -> ${suffixes.join(',')}` : prefix;
         }));
     }
-    if (soTerms.size) {
-        return [[...soTerms].join(','), [...descriptions].join(',')];
-    }
-    return [];
+    return soTerms.size
+        ? [[...soTerms].join(','), [...descriptions].join(',')]
+        : [];
 }
 function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {
         return [];
     }
-    // look for a definition with an SO type for this
     let soTerm = altTypeToSO[alt];
-    // if no SO term but ALT is in metadata, assume sequence_variant
     if (!soTerm && parser.getMetadata('ALT', alt)) {
         soTerm = 'sequence_variant';
     }
     if (soTerm) {
         return [soTerm, alt];
     }
-    // try to look for a definition for a parent term if we can
     const modAlt = alt.split(':');
     if (modAlt.length > 1) {
         return getSOAndDescFromAltDefs(`<${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
 function getSOAndDescByExamination(ref, alt) {
     const bnd = (0, vcf_1.parseBreakend)(alt);
     if (bnd) {

package/dist/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;
 }

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -3,28 +3,32 @@ 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 tabix_1 = require("@gmod/tabix");
-const vcf_1 = __importDefault(require("@gmod/vcf"));
-// local
 const VcfFeature_1 = __importDefault(require("../VcfFeature"));
 class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async configurePre() {
-        const pm = this.pluginManager;
+    async configurePre(opts) {
+        const { statusCallback = () => { } } = 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, pm);
+        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, pm) : undefined,
-            tbiFilehandle: !isCSI ? (0, io_1.openLocation)(location, pm) : undefined,
+            csiFilehandle: isCSI
+                ? (0, io_1.openLocation)(location, this.pluginManager)
+                : undefined,
+            tbiFilehandle: !isCSI
+                ? (0, io_1.openLocation)(location, this.pluginManager)
+                : undefined,
             chunkCacheSize: 50 * 2 ** 20,
         });
-        const header = await vcf.getHeader();
+        const header = await (0, util_1.updateStatus)('Downloading index', statusCallback, () => vcf.getHeader());
         return {
             vcf,
             parser: new vcf_1.default({ header }),
@@ -54,8 +58,9 @@ class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(query, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { refName, start, end } = query;
+            const { statusCallback = () => { } } = opts;
             const { vcf, parser } = await this.configure();
-            await vcf.getLines(refName, start, end, {
+            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),
@@ -64,10 +69,36 @@ class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     }));
                 },
                 ...opts,
-            });
+            }));
             observer.complete();
-        }, opts.signal);
+        }, 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 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( /* { region } */) { }
+    freeResources() { }
 }
 exports.default = VcfTabixAdapter;

package/dist/VcfTabixAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     vcfGzLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configuration
         };
     };
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.location
-         */
         location: {
             type: string;
             defaultValue: {
@@ -29,5 +20,13 @@ declare const VcfTabixAdapter: import("@jbrowse/core/configuration/configuration
             };
         };
     }, 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

@@ -1,31 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config VcfTabixAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const mobx_state_tree_1 = require("mobx-state-tree");
+function x() { }
 const VcfTabixAdapter = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapter', {
-    /**
-     * #slot
-     */
     vcfGzLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
     },
     index: (0, configuration_1.ConfigurationSchema)('VcfIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: mobx_state_tree_1.types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -34,5 +22,13 @@ const VcfTabixAdapter = (0, configuration_1.ConfigurationSchema)('VcfTabixAdapte
             },
         },
     }),
+    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 });
 exports.default = VcfTabixAdapter;

package/dist/VcfTabixAdapter/index.d.ts

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