@jbrowse/plugin-bed 2.16.1 → 2.18.0

package/dist/BedGraphTabixAdapter/index.js

@@ -0,0 +1,39 @@
+"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 (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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BedGraphTabixAdapterF;
+const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+function BedGraphTabixAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType_1.default({
+        name: 'BedGraphTabixAdapter',
+        displayName: 'BedGraphTabix adapter',
+        configSchema: configSchema_1.default,
+        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BedGraphTabixAdapter'))).then(r => r.default),
+    }));
+}

package/dist/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -1,9 +1,10 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature, Region } from '@jbrowse/core/util';
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     private parser;
     protected bed: TabixIndexedFile;

package/dist/BedTabixAdapter/BedTabixAdapter.js

@@ -4,12 +4,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const bed_1 = __importDefault(require("@gmod/bed"));
+const tabix_1 = require("@gmod/tabix");
 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");
-// locals
-const util_1 = require("../util");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
+const util_2 = require("../util");
 class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -49,24 +50,37 @@ class BedTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             : undefined;
     }
     getFeatures(query, opts = {}) {
+        const { stopToken } = opts;
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const meta = await this.bed.getMetadata();
             const { columnNumbers } = meta;
             const colRef = columnNumbers.ref - 1;
             const colStart = columnNumbers.start - 1;
             const colEnd = columnNumbers.end - 1;
-            // colSame handles special case for tabix where a single column is both
-            // the start and end, this is assumed to be covering the base at this
-            // position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same
             const names = await this.getNames();
+            let start = performance.now();
+            (0, stopToken_1.checkStopToken)(stopToken);
             await this.bed.getLines(query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset) => {
-                    observer.next((0, util_1.featureData)(line, colRef, colStart, colEnd, this.scoreColumn, this.parser, `${this.id}-${fileOffset}`, names));
+                    if (performance.now() - start > 200) {
+                        (0, stopToken_1.checkStopToken)(stopToken);
+                        start = performance.now();
+                    }
+                    observer.next(new util_1.SimpleFeature((0, util_2.featureData)({
+                        line,
+                        colRef,
+                        colStart,
+                        colEnd,
+                        scoreColumn: this.scoreColumn,
+                        parser: this.parser,
+                        uniqueId: `${this.id}-${fileOffset}`,
+                        names,
+                    })));
                 },
-                signal: opts.signal,
+                stopToken: opts.stopToken,
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/dist/BedTabixAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bedGzLocation: {
         type: string;
         defaultValue: {
@@ -10,17 +7,11 @@ declare const BedTabixAdapter: 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: {
@@ -29,25 +20,16 @@ declare const BedTabixAdapter: import("@jbrowse/core/configuration/configuration
             };
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
     columnNames: {
         type: string;
         description: string;
         defaultValue: never[];
     };
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     autoSql: {
         type: string;
         description: string;

package/dist/BedTabixAdapter/configSchema.js

@@ -2,30 +2,18 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
 const mobx_state_tree_1 = require("mobx-state-tree");
-/**
- * #config BedTabixAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BedTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedTabixAdapter', {
-    /**
-     * #slot
-     */
     bedGzLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
     },
     index: (0, configuration_1.ConfigurationSchema)('TabixIndex', {
-        /**
-         * #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: {
@@ -34,25 +22,16 @@ const BedTabixAdapter = (0, configuration_1.ConfigurationSchema)('BedTabixAdapte
             },
         },
     }),
-    /**
-     * #slot
-     */
     columnNames: {
         type: 'stringArray',
         description: 'List of column names',
         defaultValue: [],
     },
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: 'string',
         description: 'The column to use as a "score" attribute',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     autoSql: {
         type: 'string',
         description: 'The autoSql definition for the data fields in the file',

package/dist/BedTabixAdapter/index.d.ts

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

package/dist/BedpeAdapter/BedpeAdapter.d.ts

@@ -1,6 +1,8 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region, Feature, SimpleFeature } from '@jbrowse/core/util';
 import IntervalTree from '@flatten-js/interval-tree';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature } from '@jbrowse/core/util';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature, Region } from '@jbrowse/core/util';
 export declare function featureData(line: string, uniqueId: string, flip: boolean, names?: string[]): SimpleFeature;
 export default class BedpeAdapter extends BaseFeatureDataAdapter {
     protected bedpeFeatures?: Promise<{

package/dist/BedpeAdapter/BedpeAdapter.js

@@ -4,12 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.featureData = featureData;
+const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
 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 util_1 = require("@jbrowse/core/util");
-const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
 const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
 function featureData(line, uniqueId, flip, names) {
     const l = line.split('\t');
@@ -44,7 +43,7 @@ function featureData(line, uniqueId, flip, names) {
             end: end2,
             strand: strand2,
         },
-        ...(ALT ? { ALT: [ALT] } : {}), // ALT is an array in VCF
+        ...(ALT ? { ALT: [ALT] } : {}),
     });
 }
 function parseStrand(strand) {
@@ -64,12 +63,11 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         super(...arguments);
         this.intervalTrees = {};
     }
-    async loadDataP(opts = {}) {
+    async loadDataP(opts) {
         const pm = this.pluginManager;
         const bedLoc = this.getConf('bedpeLocation');
-        const buf = await (0, io_1.openLocation)(bedLoc, pm).readFile(opts);
-        const buffer = (0, util_1.isGzip)(buf) ? await (0, bgzf_filehandle_1.unzip)(buf) : buf;
-        // 512MB  max chrome string length is 512MB
+        const loc = (0, io_1.openLocation)(bedLoc, pm);
+        const buffer = await (0, util_1.fetchAndMaybeUnzip)(loc, opts);
         if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');
         }
@@ -165,7 +163,7 @@ class BedpeAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 observer.next(f);
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/dist/BedpeAdapter/configSchema.d.ts

@@ -1,8 +1,4 @@
 declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * can be plaintext or gzipped, not indexed so loaded into memory on startup
-     */
     bedpeLocation: {
         type: string;
         defaultValue: {
@@ -10,9 +6,6 @@ declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSch
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     columnNames: {
         type: string;
         description: string;

package/dist/BedpeAdapter/configSchema.js

@@ -1,16 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config BedpeAdapter
- * intended for SVs in a single assembly
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BedpeAdapter = (0, configuration_1.ConfigurationSchema)('BedpeAdapter', {
-    /**
-     * #slot
-     * can be plaintext or gzipped, not indexed so loaded into memory on startup
-     */
     bedpeLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -18,9 +10,6 @@ const BedpeAdapter = (0, configuration_1.ConfigurationSchema)('BedpeAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     columnNames: {
         type: 'stringArray',
         description: 'List of column names',

package/dist/BedpeAdapter/index.d.ts

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

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,11 +1,12 @@
 import { BigBed } from '@gmod/bbi';
 import BED from '@gmod/bed';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { Observer } from 'rxjs';
+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 { Region } from '@jbrowse/core/util/types';
+import type { Observer } from 'rxjs';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
-    private cached?;
+    private cachedP?;
     configurePre(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
         header: import("@gmod/bbi").Header;
@@ -17,6 +18,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         parser: BED;
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getData(): Promise<Feature[]>;
     getHeader(opts?: BaseOptions): Promise<{
         version: number;
         fileType: string;
@@ -25,7 +27,13 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             [k: string]: string;
         };
     }>;
-    getFeaturesHelper(query: Region, opts: BaseOptions, observer: Observer<Feature>, allowRedispatch: boolean, originalQuery?: Region): Promise<void>;
+    getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery, }: {
+        query: Region;
+        opts: BaseOptions;
+        observer: Observer<Feature>;
+        allowRedispatch: boolean;
+        originalQuery?: Region;
+    }): Promise<void>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -6,10 +6,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const bbi_1 = require("@gmod/bbi");
 const bed_1 = __importDefault(require("@gmod/bed"));
 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 util_1 = require("@jbrowse/core/util");
-// locals
+const rxjs_2 = require("rxjs");
 const util_2 = require("../util");
 class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre(opts) {
@@ -18,22 +18,42 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             filehandle: (0, io_1.openLocation)(this.getConf('bigBedLocation'), pm),
         });
         const header = await bigbed.getHeader(opts);
-        const parser = new bed_1.default({ autoSql: header.autoSql });
-        return { bigbed, header, parser };
+        const parser = new bed_1.default({
+            autoSql: header.autoSql,
+        });
+        return {
+            bigbed,
+            header,
+            parser,
+        };
     }
     async configure(opts) {
-        if (!this.cached) {
-            this.cached = this.configurePre(opts).catch((e) => {
-                this.cached = undefined;
+        if (!this.cachedP) {
+            this.cachedP = this.configurePre(opts).catch((e) => {
+                this.cachedP = undefined;
                 throw e;
             });
         }
-        return this.cached;
+        return this.cachedP;
     }
     async getRefNames(opts) {
         const { header } = await this.configure(opts);
         return Object.keys(header.refsByName);
     }
+    async getData() {
+        const refNames = await this.getRefNames();
+        const features = [];
+        for (const refName of refNames) {
+            const f = await (0, rxjs_2.firstValueFrom)(this.getFeatures({
+                assemblyName: 'unknown',
+                refName,
+                start: 0,
+                end: Number.MAX_SAFE_INTEGER,
+            }).pipe((0, rxjs_2.toArray)()));
+            features.push(f);
+        }
+        return features.flat();
+    }
     async getHeader(opts) {
         const { parser, header } = await this.configure(opts);
         const { version, fileType } = header;
@@ -45,13 +65,14 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             fields: Object.fromEntries(fields.map(({ name, comment }) => [name, comment])),
         };
     }
-    async getFeaturesHelper(query, opts, observer, allowRedispatch, originalQuery = query) {
-        const { signal } = opts;
+    async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
+        var _a;
+        const { stopToken } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
         const { parser, bigbed } = await this.configure(opts);
         const feats = await bigbed.getFeatures(query.refName, query.start, query.end, {
-            signal,
+            stopToken,
             basesPerSpan: query.end - query.start,
         });
         if (allowRedispatch && feats.length) {
@@ -66,7 +87,17 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 }
             }
             if (maxEnd > query.end || minStart < query.start) {
-                await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, observer, false, query);
+                await this.getFeaturesHelper({
+                    query: {
+                        ...query,
+                        start: minStart,
+                        end: maxEnd,
+                    },
+                    opts,
+                    observer,
+                    allowRedispatch: false,
+                    originalQuery: query,
+                });
                 return;
             }
         }
@@ -75,62 +106,36 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             throw new Error('found uniqueId undefined');
         }
         for (const feat of feats) {
-            const data = parser.parseLine(`${query.refName}\t${feat.start}\t${feat.end}\t${feat.rest}`, { uniqueId: feat.uniqueId });
+            const splitLine = [
+                query.refName,
+                `${feat.start}`,
+                `${feat.end}`,
+                ...(((_a = feat.rest) === null || _a === void 0 ? void 0 : _a.split('\t')) || []),
+            ];
+            const data = parser.parseLine(splitLine, { uniqueId: feat.uniqueId });
             const aggr = data[aggregateField];
             if (!parentAggregation[aggr]) {
                 parentAggregation[aggr] = [];
             }
-            const { uniqueId, type, chromStart, chromStarts, blockStarts, blockCount, blockSizes, chromEnd, thickStart, thickEnd, chrom, score, ...rest } = data;
-            const subfeatures = blockCount
-                ? (0, util_2.makeBlocks)({
-                    chromStarts,
-                    blockStarts,
-                    blockCount,
-                    blockSizes,
-                    uniqueId,
-                    refName: query.refName,
-                    start: feat.start,
-                })
-                : [];
-            if ((0, util_2.isUcscProcessedTranscript)(data)) {
-                const f = (0, util_2.ucscProcessedTranscript)({
-                    ...rest,
-                    uniqueId,
-                    type,
-                    start: feat.start,
-                    end: feat.end,
-                    refName: query.refName,
-                    score: scoreColumn ? +data[scoreColumn] : score,
-                    chromStarts,
-                    blockCount,
-                    blockSizes,
-                    thickStart,
-                    thickEnd,
-                    subfeatures,
-                });
-                if (aggr) {
-                    parentAggregation[aggr].push(f);
-                }
-                else {
-                    if ((0, util_1.doesIntersect2)(f.start, f.end, originalQuery.start, originalQuery.end)) {
-                        observer.next(new util_1.SimpleFeature({ id: `${this.id}-${uniqueId}`, data: f }));
-                    }
-                }
+            const { uniqueId, type, chrom, chromStart, chromEnd, description, chromStarts: chromStarts2, blockStarts: blockStarts2, blockSizes: blockSizes2, score: score2, blockCount, thickStart, thickEnd, strand, ...rest } = data;
+            const f = (0, util_2.featureData2)({
+                ...rest,
+                scoreColumn,
+                splitLine,
+                parser,
+                uniqueId,
+                start: feat.start,
+                end: feat.end,
+                refName: query.refName,
+            });
+            if (aggr) {
+                parentAggregation[aggr].push(f);
             }
             else {
-                if ((0, util_1.doesIntersect2)(feat.start, feat.end, originalQuery.start, originalQuery.end)) {
+                if ((0, util_1.doesIntersect2)(f.start, f.end, originalQuery.start, originalQuery.end)) {
                     observer.next(new util_1.SimpleFeature({
                         id: `${this.id}-${uniqueId}`,
-                        data: {
-                            ...rest,
-                            uniqueId,
-                            type,
-                            start: feat.start,
-                            score: scoreColumn ? +data[scoreColumn] : score,
-                            end: feat.end,
-                            refName: query.refName,
-                            subfeatures,
-                        },
+                        data: f,
                     }));
                 }
             }
@@ -159,12 +164,17 @@ class BigBedAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     getFeatures(query, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             try {
-                await this.getFeaturesHelper(query, opts, observer, true);
+                await this.getFeaturesHelper({
+                    query,
+                    opts,
+                    observer,
+                    allowRedispatch: true,
+                });
             }
             catch (e) {
                 observer.error(e);
             }
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/dist/BigBedAdapter/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     bigBedLocation: {
         type: string;
         defaultValue: {
@@ -9,17 +6,11 @@ declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSc
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: string;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */
     aggregateField: {
         type: string;
         description: string;

package/dist/BigBedAdapter/configSchema.js

@@ -1,29 +1,17 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config BigBedAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BigBedAdapter = (0, configuration_1.ConfigurationSchema)('BigBedAdapter', {
-    /**
-     * #slot
-     */
     bigBedLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
     },
-    /**
-     * #slot
-     */
     scoreColumn: {
         type: 'string',
         description: 'The column to use as a "score" attribute',
         defaultValue: '',
     },
-    /**
-     * #slot
-     */
     aggregateField: {
         type: 'string',
         description: 'An attribute to aggregate features with',

package/dist/BigBedAdapter/index.d.ts

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