@jbrowse/plugin-bed 2.17.0 → 2.18.0

package/esm/BedGraphAdapter/BedGraphAdapter.js

@@ -0,0 +1,124 @@
+import IntervalTree from '@flatten-js/interval-tree';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+export default class BedGraphAdapter extends BaseFeatureDataAdapter {
+    constructor() {
+        super(...arguments);
+        this.intervalTrees = {};
+    }
+    async getNames() {
+        const { header, columnNames } = await this.loadData();
+        if (columnNames.length) {
+            return columnNames;
+        }
+        const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
+        const defline = defs.at(-1);
+        return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
+            ? defline
+                .slice(1)
+                .split('\t')
+                .map(field => field.trim())
+            : undefined;
+    }
+    async loadFeatureIntervalTreeHelper(refName) {
+        var _a;
+        const { features } = await this.loadData();
+        const lines = features[refName];
+        if (!lines) {
+            return undefined;
+        }
+        const names = ((_a = (await this.getNames())) === null || _a === void 0 ? void 0 : _a.slice(3)) || [];
+        const intervalTree = new IntervalTree();
+        for (let i = 0; i < lines.length; i++) {
+            const line = lines[i];
+            const [refName, s, e, ...rest] = line.split('\t');
+            for (let j = 0; j < rest.length; j++) {
+                const uniqueId = `${this.id}-${refName}-${i}-${j}`;
+                const start = +s;
+                const end = +e;
+                const score = +rest[j];
+                const source = names[j] || `col${j}`;
+                if (score) {
+                    intervalTree.insert([start, end], new SimpleFeature({
+                        id: uniqueId,
+                        data: {
+                            refName,
+                            start,
+                            end,
+                            score,
+                            source,
+                        },
+                    }));
+                }
+            }
+        }
+        return intervalTree;
+    }
+    async getRefNames(opts = {}) {
+        const { features } = await this.loadData(opts);
+        return Object.keys(features);
+    }
+    async loadDataP(opts = {}) {
+        const pm = this.pluginManager;
+        const bedLoc = this.getConf('bedGraphLocation');
+        const buffer = await fetchAndMaybeUnzip(openLocation(bedLoc, pm), opts);
+        if (buffer.length > 536870888) {
+            throw new Error('Data exceeds maximum string length (512MB)');
+        }
+        const data = new TextDecoder('utf8', { fatal: true }).decode(buffer);
+        const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
+        const headerLines = [];
+        let i = 0;
+        for (; i < lines.length && lines[i].startsWith('#'); i++) {
+            headerLines.push(lines[i]);
+        }
+        const header = headerLines.join('\n');
+        const features = {};
+        for (; i < lines.length; i++) {
+            const line = lines[i];
+            const tab = line.indexOf('\t');
+            const refName = line.slice(0, tab);
+            if (!features[refName]) {
+                features[refName] = [];
+            }
+            features[refName].push(line);
+        }
+        const columnNames = this.getConf('columnNames');
+        return {
+            header,
+            features,
+            columnNames,
+        };
+    }
+    async loadFeatureIntervalTree(refName) {
+        if (!this.intervalTrees[refName]) {
+            this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch((e) => {
+                this.intervalTrees[refName] = undefined;
+                throw e;
+            });
+        }
+        return this.intervalTrees[refName];
+    }
+    async loadData(opts = {}) {
+        if (!this.bedFeatures) {
+            this.bedFeatures = this.loadDataP(opts).catch((e) => {
+                this.bedFeatures = undefined;
+                throw e;
+            });
+        }
+        return this.bedFeatures;
+    }
+    getFeatures(query, _opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { start, end, refName } = query;
+            const intervalTree = await this.loadFeatureIntervalTree(refName);
+            intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(f => {
+                observer.next(f);
+            });
+            observer.complete();
+        });
+    }
+    freeResources() { }
+}

package/esm/BedGraphAdapter/configSchema.d.ts

@@ -0,0 +1,15 @@
+declare const BedGraphAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    bedGraphLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    columnNames: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default BedGraphAdapter;

package/esm/BedGraphAdapter/configSchema.js

@@ -0,0 +1,17 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+function x() { }
+const BedGraphAdapter = ConfigurationSchema('BedGraphAdapter', {
+    bedGraphLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bedgraph',
+            locationType: 'UriLocation',
+        },
+    },
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+}, { explicitlyTyped: true });
+export default BedGraphAdapter;

package/esm/BedGraphAdapter/index.d.ts

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

package/esm/BedGraphAdapter/index.js

@@ -0,0 +1,10 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default function BedGraphAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'BedGraphAdapter',
+        displayName: 'BedGraph adapter',
+        configSchema,
+        getAdapterClass: () => import('./BedGraphAdapter').then(r => r.default),
+    }));
+}

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.d.ts

@@ -0,0 +1,18 @@
+import { TabixIndexedFile } from '@gmod/tabix';
+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';
+export default class BedGraphAdapter extends BaseFeatureDataAdapter {
+    private configured?;
+    private configurePre;
+    protected configure(): Promise<{
+        bedGraph: TabixIndexedFile;
+        header: string;
+        columnNames: string[];
+    }>;
+    getNames(): Promise<string[] | undefined>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(): Promise<string>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -0,0 +1,102 @@
+import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+export default class BedGraphAdapter extends BaseFeatureDataAdapter {
+    async configurePre() {
+        const pm = this.pluginManager;
+        const bedGraphGzLocation = this.getConf('bedGraphGzLocation');
+        const location = this.getConf(['index', 'location']);
+        const indexType = this.getConf(['index', 'indexType']);
+        const filehandle = openLocation(bedGraphGzLocation, pm);
+        const isCSI = indexType === 'CSI';
+        const bedGraph = new TabixIndexedFile({
+            filehandle,
+            csiFilehandle: isCSI ? openLocation(location, pm) : undefined,
+            tbiFilehandle: !isCSI ? openLocation(location, pm) : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+        });
+        const columnNames = this.getConf('columnNames');
+        const header = await bedGraph.getHeader();
+        return {
+            columnNames,
+            bedGraph,
+            header,
+        };
+    }
+    async configure() {
+        if (!this.configured) {
+            this.configured = this.configurePre().catch((e) => {
+                this.configured = undefined;
+                throw e;
+            });
+        }
+        return this.configured;
+    }
+    async getNames() {
+        const { bedGraph, columnNames } = await this.configure();
+        if (columnNames.length) {
+            return columnNames;
+        }
+        const header = await bedGraph.getHeader();
+        const defs = header.split(/\n|\r\n|\r/).filter(f => !!f);
+        const defline = defs.at(-1);
+        return (defline === null || defline === void 0 ? void 0 : defline.includes('\t'))
+            ? defline
+                .slice(1)
+                .split('\t')
+                .map(f => f.trim())
+            : undefined;
+    }
+    async getRefNames(opts = {}) {
+        const { bedGraph } = await this.configure();
+        return bedGraph.getReferenceSequenceNames(opts);
+    }
+    async getHeader() {
+        const { bedGraph } = await this.configure();
+        return bedGraph.getHeader();
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            var _a;
+            const { bedGraph } = await this.configure();
+            const meta = await bedGraph.getMetadata();
+            const { columnNumbers } = meta;
+            const colRef = columnNumbers.ref - 1;
+            const colStart = columnNumbers.start - 1;
+            const colEnd = columnNumbers.end - 1;
+            const same = colStart === colEnd;
+            const names = ((_a = (await this.getNames())) === null || _a === void 0 ? void 0 : _a.slice(same ? 2 : 3)) || [];
+            await bedGraph.getLines(query.refName, query.start + (same ? -1 : 0), query.end, {
+                lineCallback: (line, fileOffset) => {
+                    const cols = line.split('\t');
+                    const refName = cols[colRef];
+                    const start = +cols[colStart];
+                    const end = +(same ? start + 1 : cols[colEnd]);
+                    const rest = cols.slice(colEnd + 1);
+                    for (let j = 0; j < rest.length; j++) {
+                        const uniqueId = `${this.id}-${fileOffset}-${j}`;
+                        const score = Math.abs(+rest[j]);
+                        const source = names[j] || `col${j}`;
+                        if (score) {
+                            observer.next(new SimpleFeature({
+                                id: uniqueId,
+                                data: {
+                                    refName,
+                                    start,
+                                    end,
+                                    score,
+                                    source,
+                                },
+                            }));
+                        }
+                    }
+                },
+                ...opts,
+            });
+            observer.complete();
+        });
+    }
+    freeResources() { }
+}

package/esm/BedGraphTabixAdapter/configSchema.d.ts

@@ -0,0 +1,29 @@
+declare const BedGraphTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    bedGraphGzLocation: {
+        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>>;
+    columnNames: {
+        type: string;
+        description: string;
+        defaultValue: never[];
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default BedGraphTabixAdapter;

package/esm/BedGraphTabixAdapter/configSchema.js

@@ -0,0 +1,32 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { types } from 'mobx-state-tree';
+function x() { }
+const BedGraphTabixAdapter = ConfigurationSchema('BedGraphTabixAdapter', {
+    bedGraphGzLocation: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my.bedgraph',
+            locationType: 'UriLocation',
+        },
+    },
+    index: ConfigurationSchema('VcfIndex', {
+        indexType: {
+            model: types.enumeration('IndexType', ['TBI', 'CSI']),
+            type: 'stringEnum',
+            defaultValue: 'TBI',
+        },
+        location: {
+            type: 'fileLocation',
+            defaultValue: {
+                uri: '/path/to/my.vcf.gz.tbi',
+                locationType: 'UriLocation',
+            },
+        },
+    }),
+    columnNames: {
+        type: 'stringArray',
+        description: 'List of column names',
+        defaultValue: [],
+    },
+}, { explicitlyTyped: true });
+export default BedGraphTabixAdapter;

package/esm/BedGraphTabixAdapter/index.d.ts

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

package/esm/BedGraphTabixAdapter/index.js

@@ -0,0 +1,10 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export default function BedGraphTabixAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'BedGraphTabixAdapter',
+        displayName: 'BedGraphTabix adapter',
+        configSchema,
+        getAdapterClass: () => import('./BedGraphTabixAdapter').then(r => r.default),
+    }));
+}

package/esm/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/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -1,10 +1,10 @@
 import BED from '@gmod/bed';
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature, } from '@jbrowse/core/util';
-import { TabixIndexedFile } from '@gmod/tabix';
-// locals
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { featureData } from '../util';
 class BedTabixAdapter extends BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
@@ -45,6 +45,7 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
             : undefined;
     }
     getFeatures(query, opts = {}) {
+        const { stopToken } = opts;
         return ObservableCreate(async (observer) => {
             const meta = await this.bed.getMetadata();
             const { columnNumbers } = meta;
@@ -52,8 +53,14 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
             const colStart = columnNumbers.start - 1;
             const colEnd = columnNumbers.end - 1;
             const names = await this.getNames();
+            let start = performance.now();
+            checkStopToken(stopToken);
             await this.bed.getLines(query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset) => {
+                    if (performance.now() - start > 200) {
+                        checkStopToken(stopToken);
+                        start = performance.now();
+                    }
                     observer.next(new SimpleFeature(featureData({
                         line,
                         colRef,
@@ -65,10 +72,10 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
                         names,
                     })));
                 },
-                signal: opts.signal,
+                stopToken: opts.stopToken,
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/esm/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/esm/BedTabixAdapter/configSchema.js

@@ -1,29 +1,17 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-/**
- * #config BedTabixAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
-    /**
-     * #slot
-     */
     bedGzLocation: {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
     },
     index: ConfigurationSchema('TabixIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {
@@ -32,25 +20,16 @@ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
             },
         },
     }),
-    /**
-     * #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/esm/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/esm/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/esm/BedpeAdapter/BedpeAdapter.js

@@ -1,8 +1,8 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import IntervalTree from '@flatten-js/interval-tree';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { SimpleFeature, fetchAndMaybeUnzip, } from '@jbrowse/core/util';
-import IntervalTree from '@flatten-js/interval-tree';
 const svTypes = new Set(['DUP', 'TRA', 'INV', 'CNV', 'DEL']);
 export function featureData(line, uniqueId, flip, names) {
     const l = line.split('\t');
@@ -37,7 +37,7 @@ export 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) {
@@ -62,7 +62,6 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
         const bedLoc = this.getConf('bedpeLocation');
         const loc = openLocation(bedLoc, pm);
         const buffer = await fetchAndMaybeUnzip(loc, opts);
-        // 512MB  max chrome string length is 512MB
         if (buffer.length > 536870888) {
             throw new Error('Data exceeds maximum string length (512MB)');
         }
@@ -158,7 +157,7 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
                 observer.next(f);
             });
             observer.complete();
-        }, opts.signal);
+        }, opts.stopToken);
     }
     freeResources() { }
 }

package/esm/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/esm/BedpeAdapter/configSchema.js

@@ -1,14 +1,6 @@
 import { ConfigurationSchema } from '@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 = ConfigurationSchema('BedpeAdapter', {
-    /**
-     * #slot
-     * can be plaintext or gzipped, not indexed so loaded into memory on startup
-     */
     bedpeLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -16,9 +8,6 @@ const BedpeAdapter = ConfigurationSchema('BedpeAdapter', {
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     columnNames: {
         type: 'stringArray',
         description: 'List of column names',

package/esm/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;