@jbrowse/plugin-bed 3.6.5 → 4.0.0

package/esm/BedAdapter/BedAdapter.d.ts

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
@@ -14,7 +14,7 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
         colStart: number;
         colEnd: number;
     }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
     static capabilities: string[];
     private loadDataP;
     loadData(opts?: BaseOptions): Promise<{
@@ -31,6 +31,6 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
     getHeader(opts?: BaseOptions): Promise<string>;
     getNames(): Promise<string[] | undefined>;
     private loadFeatureIntervalTreeHelper;
-    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<any> | undefined>;
+    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<Feature> | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
 }

package/esm/BedAdapter/BedAdapter.js

@@ -1,16 +1,15 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { featureData } from '../util';
-class BedAdapter extends BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.intervalTrees = {};
-    }
+import { featureData } from "../util.js";
+export default class BedAdapter extends BaseFeatureDataAdapter {
+    bedFeatures;
+    intervalTrees = {};
+    static capabilities = ['getFeatures', 'getRefNames'];
     async loadDataP(opts) {
         const bedLoc = this.getConf('bedLocation');
         const buffer = await fetchAndMaybeUnzip(openLocation(bedLoc, this.pluginManager), opts);
@@ -29,7 +28,7 @@ class BedAdapter extends BaseFeatureDataAdapter {
                 features[refName].push(line);
             }
             return true;
-        }, opts === null || opts === void 0 ? void 0 : opts.statusCallback);
+        }, opts?.statusCallback);
         const header = headerLines.join('\n');
         const autoSql = this.getConf('autoSql');
         const parser = new BED({ autoSql });
@@ -73,7 +72,7 @@ class BedAdapter extends BaseFeatureDataAdapter {
         }
         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'))
+        return defline?.includes('\t')
             ? defline
                 .slice(1)
                 .split('\t')
@@ -118,7 +117,7 @@ class BedAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             const { start, end, refName } = query;
             const intervalTree = await this.loadFeatureIntervalTree(refName);
-            const features = intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]);
+            const features = intervalTree?.search([start, end]);
             if (features) {
                 for (const f of features) {
                     observer.next(f);
@@ -128,5 +127,3 @@ class BedAdapter extends BaseFeatureDataAdapter {
         }, opts.stopToken);
     }
 }
-BedAdapter.capabilities = ['getFeatures', 'getRefNames'];
-export default BedAdapter;

package/esm/BedAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const BedAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     bedLocation: {
         type: string;
         description: string;
@@ -37,5 +37,5 @@ declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchem
         description: string;
         defaultValue: number;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BedAdapter;

package/esm/BedAdapter/index.js

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

package/esm/BedGraphAdapter/BedGraphAdapter.d.ts

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 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';
@@ -8,12 +8,12 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         features: Record<string, string[]>;
         columnNames: string[];
     }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    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<any> | undefined>;
+    loadFeatureIntervalTree(refName: string): Promise<IntervalTree<Feature> | undefined>;
     loadData(opts?: BaseOptions): Promise<{
         header: string;
         features: Record<string, string[]>;

package/esm/BedGraphAdapter/BedGraphAdapter.js

@@ -1,14 +1,12 @@
-import IntervalTree from '@flatten-js/interval-tree';
+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 { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 export default class BedGraphAdapter extends BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.intervalTrees = {};
-    }
+    bedFeatures;
+    intervalTrees = {};
     async getNames() {
         const { header, columnNames } = await this.loadData();
         if (columnNames.length) {
@@ -16,7 +14,7 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         }
         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'))
+        return defline?.includes('\t')
             ? defline
                 .slice(1)
                 .split('\t')
@@ -24,18 +22,17 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
             : 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 names = (await this.getNames())?.slice(3) || [];
         const intervalTree = new IntervalTree();
-        for (let i = 0; i < lines.length; i++) {
+        for (let i = 0, l = lines.length; i < l; i++) {
             const line = lines[i];
             const [refName, s, e, ...rest] = line.split('\t');
-            for (let j = 0; j < rest.length; j++) {
+            for (let j = 0, l2 = rest.length; j < l2; j++) {
                 const uniqueId = `${this.id}-${refName}-${i}-${j}`;
                 const start = +s;
                 const end = +e;
@@ -110,7 +107,7 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             const { start, end, refName } = query;
             const intervalTree = await this.loadFeatureIntervalTree(refName);
-            for (const feature of (intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end])) || []) {
+            for (const feature of intervalTree?.search([start, end]) || []) {
                 observer.next(feature);
             }
             observer.complete();

package/esm/BedGraphAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const BedGraphAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const BedGraphAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     bedGraphLocation: {
         type: string;
         defaultValue: {
@@ -11,5 +11,5 @@ declare const BedGraphAdapter: import("@jbrowse/core/configuration/configuration
         description: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BedGraphAdapter;

package/esm/BedGraphAdapter/index.js

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

package/esm/BedGraphTabixAdapter/BedGraphTabixAdapter.js

@@ -4,6 +4,7 @@ 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 {
+    configured;
     async configurePre() {
         const pm = this.pluginManager;
         const bedGraphGzLocation = this.getConf('bedGraphGzLocation');
@@ -42,7 +43,7 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
         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'))
+        return defline?.includes('\t')
             ? defline
                 .slice(1)
                 .split('\t')
@@ -59,7 +60,6 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
     }
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
-            var _a;
             const { bedGraph } = await this.configure();
             const meta = await bedGraph.getMetadata();
             const { columnNumbers } = meta;
@@ -67,7 +67,7 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
             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)) || [];
+            const names = (await this.getNames())?.slice(same ? 2 : 3) || [];
             await bedGraph.getLines(query.refName, query.start + (same ? -1 : 0), query.end, {
                 lineCallback: (line, fileOffset) => {
                     const cols = line.split('\t');

package/esm/BedGraphTabixAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const BedGraphTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const BedGraphTabixAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     bedGraphGzLocation: {
         type: string;
         defaultValue: {
@@ -6,9 +6,9 @@ declare const BedGraphTabixAdapter: import("@jbrowse/core/configuration/configur
             locationType: string;
         };
     };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    index: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         indexType: {
-            model: import("mobx-state-tree").ISimpleType<string>;
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
@@ -19,11 +19,11 @@ declare const BedGraphTabixAdapter: import("@jbrowse/core/configuration/configur
                 locationType: string;
             };
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     columnNames: {
         type: string;
         description: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BedGraphTabixAdapter;

package/esm/BedGraphTabixAdapter/configSchema.js

@@ -1,5 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 function x() { }
 const BedGraphTabixAdapter = ConfigurationSchema('BedGraphTabixAdapter', {
     bedGraphGzLocation: {

package/esm/BedGraphTabixAdapter/index.js

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

package/esm/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -25,7 +25,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             [key: string]: any;
             refNameToId: Record<string, number>;
             refIdToName: string[];
-            metaChar: string | null;
+            metaChar: string | undefined;
             columnNumbers: {
                 ref: number;
                 start: number;

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -5,8 +5,14 @@ import { SimpleFeature, updateStatus } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { checkStopToken } from '@jbrowse/core/util/stopToken';
-import { featureData } from '../util';
-class BedTabixAdapter extends BaseFeatureDataAdapter {
+import { featureData } from "../util.js";
+export default class BedTabixAdapter extends BaseFeatureDataAdapter {
+    parser;
+    bed;
+    columnNames;
+    scoreColumn;
+    static capabilities = ['getFeatures', 'getRefNames'];
+    setupP;
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         const bedGzLoc = this.getConf('bedGzLocation');
@@ -54,7 +60,7 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
         const header = await this.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'))
+        return defline?.includes('\t')
             ? defline
                 .slice(1)
                 .split('\t')
@@ -74,7 +80,7 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
             checkStopToken(stopToken);
             await updateStatus('Downloading features', statusCallback, () => this.bed.getLines(query.refName, query.start, query.end, {
                 lineCallback: (line, fileOffset) => {
-                    if (performance.now() - start > 200) {
+                    if (performance.now() - start > 500) {
                         checkStopToken(stopToken);
                         start = performance.now();
                     }
@@ -95,5 +101,3 @@ class BedTabixAdapter extends BaseFeatureDataAdapter {
         }, stopToken);
     }
 }
-BedTabixAdapter.capabilities = ['getFeatures', 'getRefNames'];
-export default BedTabixAdapter;

package/esm/BedTabixAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const BedTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const BedTabixAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     bedGzLocation: {
         type: string;
         defaultValue: {
@@ -6,9 +6,9 @@ declare const BedTabixAdapter: import("@jbrowse/core/configuration/configuration
             locationType: string;
         };
     };
-    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    index: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
         indexType: {
-            model: import("mobx-state-tree").ISimpleType<string>;
+            model: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
@@ -19,7 +19,7 @@ declare const BedTabixAdapter: import("@jbrowse/core/configuration/configuration
                 locationType: string;
             };
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
     columnNames: {
         type: string;
         description: string;
@@ -35,5 +35,5 @@ declare const BedTabixAdapter: import("@jbrowse/core/configuration/configuration
         description: string;
         defaultValue: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BedTabixAdapter;

package/esm/BedTabixAdapter/configSchema.js

@@ -1,5 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 function x() { }
 const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
     bedGzLocation: {

package/esm/BedTabixAdapter/index.js

@@ -1,10 +1,10 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function BedTabixAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'BedTabixAdapter',
         displayName: 'BED tabix adapter',
         configSchema,
-        getAdapterClass: () => import('./BedTabixAdapter').then(r => r.default),
+        getAdapterClass: () => import("./BedTabixAdapter.js").then(r => r.default),
     }));
 }

package/esm/BedpeAdapter/BedpeAdapter.d.ts

@@ -1,4 +1,4 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 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';
@@ -9,7 +9,7 @@ export default class BedpeAdapter extends BaseFeatureDataAdapter {
         feats2: Record<string, string[]>;
         columnNames: string[];
     }>;
-    protected intervalTrees: Record<string, Promise<IntervalTree | undefined> | undefined>;
+    protected intervalTrees: Record<string, Promise<IntervalTree<Feature> | undefined> | undefined>;
     static capabilities: string[];
     private loadDataP;
     private loadData;

package/esm/BedpeAdapter/BedpeAdapter.js

@@ -1,14 +1,13 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { featureData } from './util';
-class BedpeAdapter extends BaseFeatureDataAdapter {
-    constructor() {
-        super(...arguments);
-        this.intervalTrees = {};
-    }
+import { featureData } from "./util.js";
+export default class BedpeAdapter extends BaseFeatureDataAdapter {
+    bedpeFeatures;
+    intervalTrees = {};
+    static capabilities = ['getFeatures', 'getRefNames'];
     async loadDataP(opts) {
         const data = await fetchAndMaybeUnzipText(openLocation(this.getConf('bedpeLocation'), this.pluginManager), opts);
         const lines = data.split(/\n|\r\n|\r/).filter(f => !!f);
@@ -66,7 +65,7 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
         }
         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'))
+        return defline?.includes('\t')
             ? defline
                 .slice(1)
                 .split('\t')
@@ -74,12 +73,11 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
             : undefined;
     }
     async loadFeatureTreeP(refName) {
-        var _a, _b, _c, _d;
         const { feats1, feats2 } = await this.loadData();
         const names = await this.getNames();
         const intervalTree = new IntervalTree();
-        const ret1 = (_b = (_a = feats1[refName]) === null || _a === void 0 ? void 0 : _a.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r1`, false, names))) !== null && _b !== void 0 ? _b : [];
-        const ret2 = (_d = (_c = feats2[refName]) === null || _c === void 0 ? void 0 : _c.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r2`, true, names))) !== null && _d !== void 0 ? _d : [];
+        const ret1 = feats1[refName]?.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r1`, false, names)) ?? [];
+        const ret2 = feats2[refName]?.map((f, i) => featureData(f, `${this.id}-${refName}-${i}-r2`, true, names)) ?? [];
         for (const obj of [...ret1, ...ret2]) {
             intervalTree.insert([obj.get('start'), obj.get('end')], obj);
         }
@@ -98,12 +96,10 @@ class BedpeAdapter extends BaseFeatureDataAdapter {
         return ObservableCreate(async (observer) => {
             const { start, end, refName } = query;
             const intervalTree = await this.loadFeatureTree(refName);
-            for (const f of (intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end])) || []) {
+            for (const f of intervalTree?.search([start, end]) || []) {
                 observer.next(f);
             }
             observer.complete();
         }, opts.stopToken);
     }
 }
-BedpeAdapter.capabilities = ['getFeatures', 'getRefNames'];
-export default BedpeAdapter;

package/esm/BedpeAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const BedpeAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     bedpeLocation: {
         type: string;
         description: string;
@@ -12,5 +12,5 @@ declare const BedpeAdapter: import("@jbrowse/core/configuration/configurationSch
         description: string;
         defaultValue: never[];
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BedpeAdapter;

package/esm/BedpeAdapter/index.js

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

package/esm/BedpeAdapter/util.js

@@ -9,7 +9,7 @@ export function featureData(line, uniqueId, flip, names) {
     const start2 = +l[!flip ? 4 : 1];
     const end2 = +l[!flip ? 5 : 2];
     const name = l[6];
-    const score = +l[7];
+    const score = l[7] ? +l[7] : undefined;
     const strand1 = parseStrand(l[8]);
     const strand2 = parseStrand(l[9]);
     const extra = l.slice(10);

package/esm/BigBedAdapter/BigBedAdapter.d.ts

@@ -9,7 +9,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     private cachedP?;
     configurePre(opts?: BaseOptions): Promise<{
         bigbed: BigBed;
-        header: import("@gmod/bbi/dist/types").BigWigHeaderWithRefNames;
+        header: import("@gmod/bbi").BigWigHeaderWithRefNames;
         parser: BED;
     }>;
     configure(opts?: BaseOptions): Promise<{

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -5,8 +5,9 @@ import { SimpleFeature, doesIntersect2, max, min, updateStatus, } from '@jbrowse
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { firstValueFrom, toArray } from 'rxjs';
-import { featureData2 } from '../util';
+import { featureData2 } from "../util.js";
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
+    cachedP;
     async configurePre(opts) {
         const pm = this.pluginManager;
         const bigbed = new BigBed({
@@ -90,7 +91,6 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
             basesPerSpan: query.end - query.start,
         }));
         await updateStatus('Processing features', statusCallback, async () => {
-            var _a;
             const parentAggregation = {};
             const parentAggregationFlat = [];
             if (feats.some(f => f.uniqueId === undefined)) {
@@ -101,7 +101,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                     query.refName,
                     `${feat.start}`,
                     `${feat.end}`,
-                    ...(((_a = feat.rest) === null || _a === void 0 ? void 0 : _a.split('\t')) || []),
+                    ...(feat.rest?.split('\t') || []),
                 ];
                 const data = parser.parseLine(splitLine, {
                     uniqueId: feat.uniqueId,
@@ -150,8 +150,8 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                     await this.getFeaturesHelper({
                         query: {
                             ...query,
-                            start: minStart - 500000,
-                            end: maxEnd + 500000,
+                            start: minStart - 500_000,
+                            end: maxEnd + 500_000,
                         },
                         opts,
                         observer,
@@ -162,18 +162,17 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                 }
             }
             Object.entries(parentAggregation).map(([name, subfeatures]) => {
-                var _a, _b, _c;
                 const s = min(subfeatures.map(f => f.start));
                 const e = max(subfeatures.map(f => f.end));
                 if (doesIntersect2(s, e, originalQuery.start, originalQuery.end)) {
                     const subs = subfeatures.sort((a, b) => a.uniqueId.localeCompare(b.uniqueId));
                     if (subs.some((a, i) => subs.some((b, j) => i !== j && doesIntersect2(a.start, a.end, b.start, b.end)))) {
                         observer.next(new SimpleFeature({
-                            id: `${this.id}-${(_a = subs[0]) === null || _a === void 0 ? void 0 : _a.uniqueId}-parent`,
+                            id: `${this.id}-${subs[0]?.uniqueId}-parent`,
                             data: {
                                 type: 'gene',
                                 subfeatures: subs,
-                                strand: ((_b = subs[0]) === null || _b === void 0 ? void 0 : _b.strand) || 1,
+                                strand: subs[0]?.strand || 1,
                                 name,
                                 start: s,
                                 end: e,
@@ -188,7 +187,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                                 data: {
                                     type: 'gene',
                                     subfeatures: [sub],
-                                    strand: ((_c = subs[0]) === null || _c === void 0 ? void 0 : _c.strand) || 1,
+                                    strand: subs[0]?.strand || 1,
                                     name,
                                     start: sub.start,
                                     end: sub.end,

package/esm/BigBedAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const BigBedAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     bigBedLocation: {
         type: string;
         defaultValue: {
@@ -16,5 +16,5 @@ declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSc
         description: string;
         defaultValue: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BigBedAdapter;

package/esm/BigBedAdapter/index.js

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