@jbrowse/plugin-bed 2.0.0 → 2.1.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.0.0",
+  "version": "2.1.2",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,15 +37,14 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@babel/runtime": "^7.17.9",
     "@flatten-js/interval-tree": "^1.0.15",
-    "@gmod/bbi": "^1.0.35",
-    "@gmod/bed": "^2.0.6",
+    "@gmod/bbi": "^2.0.2",
+    "@gmod/bed": "^2.1.2",
     "@gmod/bgzf-filehandle": "^1.4.3",
     "@gmod/tabix": "^1.5.2"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^1.0.0",
+    "@jbrowse/core": "^2.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -57,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
+  "gitHead": "449b17325c9a4a97181f7ddddf48e80219f03b8d"
 }

package/src/BedAdapter/BedAdapter.ts

@@ -18,7 +18,7 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
   protected bedFeatures?: Promise<{
     header: string
     features: Record<string, string[]>
-    parser: typeof BED
+    parser: BED
     columnNames: string[]
     scoreColumn: string
     colRef: number

package/src/BedTabixAdapter/BedTabixAdapter.ts

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import BED from '@gmod/bed'
 import {
   BaseFeatureDataAdapter,
@@ -14,7 +13,7 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
-  private parser: any
+  private parser: BED
 
   protected bed: TabixIndexedFile
 

package/src/BigBedAdapter/BigBedAdapter.ts

@@ -17,20 +17,8 @@ function isUCSC(f: Feature) {
   return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0
 }
 
-interface BEDFeature {
-  chrom: string
-  chromStart: number
-  chromEnd: number
-  [key: string]: any
-}
-
-interface Parser {
-  parseLine: (line: string, opts: { uniqueId: string | number }) => BEDFeature
-  autoSql: { fields: { name: string; comment: string }[] }
-}
-
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
-  private cached?: Promise<{ bigbed: BigBed; header: any; parser: Parser }>
+  private cached?: Promise<{ bigbed: BigBed; header: any; parser: BED }>
 
   public async configurePre(opts?: BaseOptions) {
     const bigbed = new BigBed({
@@ -40,7 +28,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
       ),
     })
     const header = await bigbed.getHeader(opts)
-    const parser = new BED({ autoSql: header.autoSql }) as Parser
+    const parser = new BED({ autoSql: header.autoSql })
     return { bigbed, header, parser }
   }
 

package/src/util.ts

@@ -130,7 +130,7 @@ export function featureData(
   colStart: number,
   colEnd: number,
   scoreColumn: string,
-  parser: typeof BED,
+  parser: BED,
   uniqueId: string,
   names?: string[],
 ) {

package/src/declare.d.ts

@@ -1 +0,0 @@
-declare module '@gmod/bed'