Add ability to use a BigBed file as a cytobands adapter

packages/core/data_adapters/CytobandAdapter/CytobandAdapter.ts

@@ -25,8 +25,9 @@ export default class CytobandAdapter extends BaseAdapter {
           refName: refName!,
           start: +start!,
           end: +end!,
-          name: name!,
-          type: type!,
+          name,
+          type,
+          gieStain: type || name,
         })
       })
   }

plugins/bed/src/BigBedAdapter/BigBedAdapter.ts

@@ -15,7 +15,7 @@ import {
   SimpleFeature,
   SimpleFeatureSerializedNoId,
 } from '@jbrowse/core/util'
-import { Observer } from 'rxjs'
+import { firstValueFrom, Observer, toArray } from 'rxjs'
 
 // locals
 import {
@@ -64,6 +64,23 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
     return Object.keys(header.refsByName)
   }
 
+  public async getData() {
+    const refNames = await this.getRefNames()
+    const features = []
+    for (const refName of refNames) {
+      const f = await firstValueFrom(
+        this.getFeatures({
+          assemblyName: 'unknown',
+          refName,
+          start: 0,
+          end: Number.MAX_SAFE_INTEGER,
+        }).pipe(toArray()),
+      )
+      features.push(f)
+    }
+    return features.flat()
+  }
+
   async getHeader(opts?: BaseOptions) {
     const { parser, header } = await this.configure(opts)
     const { version, fileType } = header

plugins/linear-genome-view/src/LinearGenomeView/components/util.ts

@@ -70,7 +70,7 @@ export function getCytobands(assembly: Assembly | undefined, refName: string) {
           assembly.getCanonicalRefName(f.get('refName')) || f.get('refName'),
         start: f.get('start'),
         end: f.get('end'),
-        type: f.get('type') as string,
+        type: f.get('gieStain') as string,
       }))
       .filter(f => f.refName === refName) || []
   )