@jbrowse/plugin-bed 5.0.0-beta.1 → 5.0.0-beta.10

package/esm/BedAdapter/BedAdapter.d.ts

@@ -1,5 +1,4 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { IntervalTree } from '@jbrowse/core/util';
 import type { BedAdapterConfig } from './configSchema.ts';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
@@ -9,13 +8,12 @@ export default class BedAdapter extends BaseFeatureDataAdapter<BedAdapterConfig>
         features: Record<string, string[]>;
     }>;
     private getParser;
-    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
     static capabilities: string[];
     private loadDataP;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
     getNames(): Promise<string[] | undefined>;
     private loadFeatureIntervalTreeHelper;
-    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<Feature> | undefined>;
+    private treeFeatures;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
 }

package/esm/BedAdapter/BedAdapter.js

@@ -14,7 +14,6 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
             columnNames: await this.getNames(),
         }),
     });
-    intervalTrees = {};
     static capabilities = ['getFeatures', 'getRefNames'];
     async loadDataP(opts) {
         const buffer = await fetchAndMaybeUnzip(openLocation(this.getConf('bedLocation'), this.pluginManager), opts);
@@ -60,14 +59,8 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
         }
         return intervalTree;
     }
-    async loadFeatureIntervalTree(refName) {
-        this.intervalTrees[refName] ??= this.loadFeatureIntervalTreeHelper(refName).catch((e) => {
-            this.intervalTrees[refName] = undefined;
-            throw e;
-        });
-        return this.intervalTrees[refName];
-    }
-    getFeatures(query, opts = {}) {
-        return intervalTreeFeatures(query, opts, refName => this.loadFeatureIntervalTree(refName));
+    treeFeatures = intervalTreeFeatures(opts => this.loadData(opts), refName => this.loadFeatureIntervalTreeHelper(refName));
+    getFeatures(query, opts) {
+        return this.treeFeatures(query, opts);
     }
 }

package/esm/BedAdapter/configSchema.d.ts

@@ -23,73 +23,51 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly bedLocation: {
-        readonly type: "fileLocation";
-        readonly description: "path to bed file, also allows gzipped bed";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.bed.gz";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly columnNames: {
-        readonly type: "stringArray";
-        readonly description: "List of column names. A column named like a standard BED column is parsed as that column's type (chromStart numeric, blockSizes a numeric list); any other column is text";
-        readonly defaultValue: readonly [];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly scoreColumn: {
-        readonly type: "string";
-        readonly description: "The column to use as a \"score\" attribute";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly autoSql: {
-        readonly type: "string";
-        readonly description: "The autoSql definition for the data fields in the file";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly colRef: {
-        readonly type: "number";
-        readonly description: "The column to use as a \"refName\" attribute";
-        readonly defaultValue: 0;
+        type: "number";
+    } & {
+        defaultValue: number;
     };
-    /**
-     * #slot
-     */
     readonly colStart: {
-        readonly type: "number";
-        readonly description: "The column to use as a \"start\" attribute";
-        readonly defaultValue: 1;
+        type: "number";
+    } & {
+        defaultValue: number;
     };
-    /**
-     * #slot
-     */
     readonly colEnd: {
-        readonly type: "number";
-        readonly description: "The column to use as a \"end\" attribute";
-        readonly defaultValue: 2;
+        type: "number";
+    } & {
+        defaultValue: number;
     };
-    /**
-     * #slot
-     */
     readonly disableGeneHeuristic: {
-        readonly type: "boolean";
-        readonly description: "Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)";
-        readonly defaultValue: false;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
 export type BedAdapterConfig = Instance<typeof BedAdapter>;
 export default BedAdapter;

package/esm/BedAdapter/configSchema.js

@@ -1,8 +1,6 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, expandUriShorthand, } from '@jbrowse/core/configuration';
 export function normalizeSnapshot(snap) {
-    return snap.uri
-        ? { ...snap, bedLocation: { uri: snap.uri, baseUri: snap.baseUri } }
-        : snap;
+    return expandUriShorthand(snap, 'bedLocation');
 }
 /**
  * #config BedAdapter

package/esm/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -1,5 +1,4 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { IntervalTree } from '@jbrowse/core/util';
 import type { BedGraphAdapterConfig } from './configSchema.ts';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
@@ -8,11 +7,10 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter<BedGraphAdap
         header: string;
         features: Record<string, string[]>;
     }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
     getNames(): Promise<string[] | undefined>;
     private loadFeatureIntervalTreeHelper;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     private loadDataP;
-    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<Feature> | undefined>;
+    private treeFeatures;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
 }

package/esm/BedGraphAdapter/BedGraphAdapter.js

@@ -7,7 +7,6 @@ import { bucketBedLines, resolveColumnNames } from '../util.js';
 export default class BedGraphAdapter extends BaseFeatureDataAdapter {
     // No `label`: `fetchAndMaybeUnzip` narrates the download from inside.
     loadData = cachedSetup({ setup: opts => this.loadDataP(opts) });
-    intervalTrees = {};
     async getNames() {
         return resolveColumnNames(this.getConf('columnNames'), async () => (await this.loadData()).header);
     }
@@ -18,12 +17,16 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
             return undefined;
         }
         const names = (await this.getNames())?.slice(3) ?? [];
+        const sourceColumn = names.indexOf('source');
         const intervalTree = new IntervalTree();
         for (let i = 0, l = lines.length; i < l; i++) {
             const [refName, s, e, ...rest] = lines[i].split('\t');
             const start = +s;
             const end = +e;
             for (let j = 0, l2 = rest.length; j < l2; j++) {
+                if (j === sourceColumn) {
+                    continue;
+                }
                 const feat = makeBedGraphFeature({
                     uniqueId: `${this.id}-${refName}-${i}-${j}`,
                     refName: refName,
@@ -32,6 +35,7 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
                     names,
                     j,
                     value: rest[j],
+                    rowSource: rest[sourceColumn],
                 });
                 if (feat) {
                     intervalTree.insert([start, end], feat);
@@ -48,14 +52,8 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         const buffer = await fetchAndMaybeUnzip(openLocation(this.getConf('bedGraphLocation'), this.pluginManager), opts);
         return bucketBedLines(buffer, opts.statusCallback);
     }
-    async loadFeatureIntervalTree(refName) {
-        this.intervalTrees[refName] ??= this.loadFeatureIntervalTreeHelper(refName).catch((e) => {
-            this.intervalTrees[refName] = undefined;
-            throw e;
-        });
-        return this.intervalTrees[refName];
-    }
-    getFeatures(query, opts = {}) {
-        return intervalTreeFeatures(query, opts, refName => this.loadFeatureIntervalTree(refName));
+    treeFeatures = intervalTreeFeatures(opts => this.loadData(opts), refName => this.loadFeatureIntervalTreeHelper(refName));
+    getFeatures(query, opts) {
+        return this.treeFeatures(query, opts);
     }
 }

package/esm/BedGraphAdapter/configSchema.d.ts

@@ -6,6 +6,9 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * #fileFormat quantitative | BedGraph (plain) | Loaded entirely into memory; for small files
  * used to load plain-text bedGraph signal files. Loads the whole file into
  * memory, so prefer the BedGraphTabixAdapter for large files.
+ * Several signals in one file are a `MultiQuantitativeTrack`'s subtracks:
+ * one value column each, named by the header, or a `source` column naming each
+ * row's, which is the form Save track data writes.
  *
  * #example
  * ```js
@@ -16,26 +19,21 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BedGraphAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * location of the plain-text bedGraph (`chrom start end value`, one line
-     * per interval). May be gzipped.
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly bedGraphLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.bedgraph";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly columnNames: {
-        readonly type: "stringArray";
-        readonly description: "List of column names";
-        readonly defaultValue: readonly [];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
 export type BedGraphAdapterConfig = Instance<typeof BedGraphAdapter>;
 export default BedGraphAdapter;

package/esm/BedGraphAdapter/configSchema.js

@@ -1,14 +1,6 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, expandUriShorthand, } from '@jbrowse/core/configuration';
 export function normalizeSnapshot(snap) {
-    return snap.uri
-        ? {
-            ...snap,
-            bedGraphLocation: {
-                uri: snap.uri,
-                baseUri: snap.baseUri,
-            },
-        }
-        : snap;
+    return expandUriShorthand(snap, 'bedGraphLocation');
 }
 /**
  * #config BedGraphAdapter
@@ -16,6 +8,9 @@ export function normalizeSnapshot(snap) {
  * #fileFormat quantitative | BedGraph (plain) | Loaded entirely into memory; for small files
  * used to load plain-text bedGraph signal files. Loads the whole file into
  * memory, so prefer the BedGraphTabixAdapter for large files.
+ * Several signals in one file are a `MultiQuantitativeTrack`'s subtracks:
+ * one value column each, named by the header, or a `source` column naming each
+ * row's, which is the form Save track data writes.
  *
  * #example
  * ```js

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -5,7 +5,6 @@ import { sharedBgzfWorkerPool } from '@jbrowse/core/util/bgzfWorkerPool';
 import { decompressedBytesBudget } from '@jbrowse/core/util/cacheBudgets';
 import { openLocation, openTabixIndexFilehandle } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { withStopTokenSignal } from '@jbrowse/core/util/stopToken';
 import { readTabixHeaderLines } from '@jbrowse/core/util/tabix';
 import { makeBedGraphFeature } from '../bedGraphUtil.js';
 import { parseNamesFromHeader } from '../util.js';
@@ -61,7 +60,8 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
             const colEnd = columnNumbers.end - 1;
             const same = colStart === colEnd;
             const names = (await this.getNames())?.slice(same ? 2 : 3) ?? [];
-            await withStopTokenSignal(opts.stopToken, signal => downloadStatus('Downloading features', opts.statusCallback, onProgress => 
+            const sourceColumn = names.indexOf('source');
+            await downloadStatus('Downloading features', opts.statusCallback, onProgress => 
             // `same` is a single-coordinate file — a GWAS-style txt with only a
             // start column, indexed `-b N -e N`. The widening is not slop: the
             // column value is used below as an interbase start (point p is
@@ -85,6 +85,9 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
                         throw new Error(`start/end NaN on line "${line}", with colStart:${colStart} and colEnd:${colEnd}. run "tabix -p bed" to ensure bed preset`);
                     }
                     for (let j = 0; j < rest.length; j++) {
+                        if (j === sourceColumn) {
+                            continue;
+                        }
                         const feat = makeBedGraphFeature({
                             uniqueId: `${this.id}-${fileOffset}-${j}`,
                             refName,
@@ -93,6 +96,7 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
                             names,
                             j,
                             value: rest[j],
+                            rowSource: rest[sourceColumn],
                         });
                         if (feat) {
                             observer.next(feat);
@@ -101,9 +105,8 @@ export default class BedGraphTabixAdapter extends BaseFeatureDataAdapter {
                 },
                 ...opts,
                 onProgress,
-                signal,
-            })));
+            }));
             observer.complete();
-        }, opts.stopToken);
+        }, opts.signal);
     }
 }

package/esm/BedGraphTabixAdapter/configSchema.d.ts

@@ -4,7 +4,10 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * #config BedGraphTabixAdapter
  * #trackType QuantitativeTrack
  * #fileFormat quantitative | BedGraph (tabix)
- * used to load bgzip-compressed, tabix-indexed bedGraph signal files
+ * used to load bgzip-compressed, tabix-indexed bedGraph signal files.
+ * Several signals in one file are a `MultiQuantitativeTrack`'s subtracks:
+ * one value column each, named by the header, or a `source` column naming each
+ * row's, which is the form Save track data writes.
  *
  * #example
  * The `uri` shorthand auto-resolves the `.tbi` index:
@@ -16,43 +19,35 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BedGraphTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * location of the bgzip-compressed bedGraph (`chrom start end value`,
-     * sorted by position). Must be bgzip rather than plain gzip, which tabix
-     * cannot index.
-     */
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly bedGraphGzLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.bedgraph";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
     readonly index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly indexType: {
-            readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"CSI" | "TBI">;
-            readonly type: 'stringEnum';
-            readonly defaultValue: 'TBI';
-            readonly description: '`TBI` is the usual `tabix` output. `CSI` is required for a reference longer than 512 Mb, which TBI cannot address.';
+            type: "stringEnum";
+        } & {
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<"CSI" | "TBI">;
+        } & {
+            defaultValue: string;
         };
         readonly location: {
-            readonly type: 'fileLocation';
-            readonly defaultValue: {
-                readonly uri: '/path/to/my.gz.tbi';
-                readonly locationType: 'UriLocation';
-            };
-            readonly description: 'location of the tabix index. Only needed when it is not named `<file>.tbi` (or `.csi`), which is what the `uri` shorthand assumes.';
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     readonly columnNames: {
-        readonly type: "stringArray";
-        readonly description: "List of column names";
-        readonly defaultValue: readonly [];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
 export type BedGraphTabixAdapterConfig = Instance<typeof BedGraphTabixAdapter>;
 export default BedGraphTabixAdapter;

package/esm/BedGraphTabixAdapter/configSchema.js

@@ -1,4 +1,4 @@
-import { ConfigurationSchema, expandTabixShorthand, tabixIndexFields, } from '@jbrowse/core/configuration';
+import { ConfigurationSchema, expandTabixShorthand, tabixIndexSchema, } from '@jbrowse/core/configuration';
 export function normalizeSnapshot(snap) {
     return expandTabixShorthand(snap, 'bedGraphGzLocation');
 }
@@ -6,7 +6,10 @@ export function normalizeSnapshot(snap) {
  * #config BedGraphTabixAdapter
  * #trackType QuantitativeTrack
  * #fileFormat quantitative | BedGraph (tabix)
- * used to load bgzip-compressed, tabix-indexed bedGraph signal files
+ * used to load bgzip-compressed, tabix-indexed bedGraph signal files.
+ * Several signals in one file are a `MultiQuantitativeTrack`'s subtracks:
+ * one value column each, named by the header, or a `source` column naming each
+ * row's, which is the form Save track data writes.
  *
  * #example
  * The `uri` shorthand auto-resolves the `.tbi` index:
@@ -31,7 +34,12 @@ const BedGraphTabixAdapter = ConfigurationSchema('BedGraphTabixAdapter', {
             locationType: 'UriLocation',
         },
     },
-    index: ConfigurationSchema('TabixIndex', { ...tabixIndexFields }),
+    /**
+     * #slot
+     * where the tabix index is and which kind it is. The `uri` shorthand derives
+     * both, so a config using it states neither.
+     */
+    index: tabixIndexSchema(),
     /**
      * #slot
      */

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -2,11 +2,11 @@ import { TabixIndexedFile } from '@gmod/tabix';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { BaseFeatureDataAdapter, cachedSetup, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { SimpleFeature, downloadStatus } from '@jbrowse/core/util';
+import { checkAbortSignal } from '@jbrowse/core/util/aborting';
 import { sharedBgzfWorkerPool } from '@jbrowse/core/util/bgzfWorkerPool';
 import { decompressedBytesBudget } from '@jbrowse/core/util/cacheBudgets';
 import { openLocation, openTabixIndexFilehandle } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { checkStopTokenThrottled, checkStopToken, createStopTokenChecker, withStopTokenSignal, } from '@jbrowse/core/util/stopToken';
 import { readTabixHeaderLines } from '@jbrowse/core/util/tabix';
 import { featureData, makeParser, parseNamesFromHeader } from '../util.js';
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
@@ -72,7 +72,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
         return parseNamesFromHeader((await readTabixHeaderLines(this.bed)).join('\n'));
     }
     getFeatures(query, opts) {
-        const { stopToken, statusCallback } = opts ?? {};
+        const { signal, statusCallback } = opts ?? {};
         return ObservableCreate(async (observer) => {
             // warms the index under its own status label — getLines would otherwise
             // download it under "Downloading features"
@@ -81,9 +81,8 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             const parser = await this.getParser();
             const scoreColumn = readConfObject(this.config, 'scoreColumn');
             const disableGeneHeuristic = readConfObject(this.config, 'disableGeneHeuristic');
-            const stopTokenCheck = createStopTokenChecker(stopToken);
-            checkStopToken(stopToken);
-            await withStopTokenSignal(stopToken, signal => downloadStatus('Downloading features', statusCallback, onProgress => 
+            checkAbortSignal(signal);
+            await downloadStatus('Downloading features', statusCallback, onProgress => 
             // start/end come from @gmod/tabix rather than being re-derived from
             // the line: it located the coordinate columns to find these lines at
             // all, and already applied the index's coordinate offset (-1 for a
@@ -92,7 +91,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             // — getLines only calls back for lines whose ref column matches it.
             this.bed.getLines(query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset, start, end) => {
-                    checkStopTokenThrottled(stopTokenCheck);
+                    checkAbortSignal(signal);
                     const splitLine = line.split('\t');
                     observer.next(new SimpleFeature(featureData({
                         splitLine,
@@ -108,8 +107,8 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
                 },
                 onProgress,
                 signal,
-            })));
+            }));
             observer.complete();
-        }, stopToken);
+        }, signal);
     }
 }

package/esm/BedTabixAdapter/configSchema.d.ts

@@ -16,66 +16,53 @@ export declare function normalizeSnapshot(snap: Record<string, unknown>): Record
  * ```
  */
 declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     * location of the bgzip-compressed BED, sorted by position. Must be bgzip
-     * rather than plain gzip, which tabix cannot index.
-     */
+    readonly densityAdapter: {
+        type: "maybeFrozen";
+    };
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
     readonly bedGzLocation: {
-        readonly type: "fileLocation";
-        readonly defaultValue: {
-            readonly uri: "/path/to/my.bed.gz";
-            readonly locationType: "UriLocation";
-        };
+        type: "fileLocation";
+    } & {
+        defaultValue: unknown;
     };
     readonly index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly indexType: {
-            readonly model: import("@jbrowse/mobx-state-tree").ISimpleType<"CSI" | "TBI">;
-            readonly type: 'stringEnum';
-            readonly defaultValue: 'TBI';
-            readonly description: '`TBI` is the usual `tabix` output. `CSI` is required for a reference longer than 512 Mb, which TBI cannot address.';
+            type: "stringEnum";
+        } & {
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<"CSI" | "TBI">;
+        } & {
+            defaultValue: string;
         };
         readonly location: {
-            readonly type: 'fileLocation';
-            readonly defaultValue: {
-                readonly uri: '/path/to/my.gz.tbi';
-                readonly locationType: 'UriLocation';
-            };
-            readonly description: 'location of the tabix index. Only needed when it is not named `<file>.tbi` (or `.csi`), which is what the `uri` shorthand assumes.';
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    /**
-     * #slot
-     */
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     readonly columnNames: {
-        readonly type: "stringArray";
-        readonly description: "List of column names. A column named like a standard BED column is parsed as that column's type (chromStart numeric, blockSizes a numeric list); any other column is text";
-        readonly defaultValue: readonly [];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
-    /**
-     * #slot
-     */
     readonly scoreColumn: {
-        readonly type: "string";
-        readonly description: "The column to use as a \"score\" attribute";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly autoSql: {
-        readonly type: "string";
-        readonly description: "The autoSql definition for the data fields in the file";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
-    /**
-     * #slot
-     */
     readonly disableGeneHeuristic: {
-        readonly type: "boolean";
-        readonly description: "Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)";
-        readonly defaultValue: false;
+        type: "boolean";
+    } & {
+        defaultValue: boolean;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
 export type BedTabixAdapterConfig = Instance<typeof BedTabixAdapter>;
 export default BedTabixAdapter;