@jbrowse/plugin-bed 1.4.3 → 1.5.2

package/src/BigBedAdapter/configSchema.ts

@@ -5,7 +5,7 @@ export default ConfigurationSchema(
   {
     bigBedLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.bb' },
+      defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },
     },
   },
   { explicitlyTyped: true },

package/src/index.ts

@@ -3,6 +3,13 @@ import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { configSchema as bigBedAdapterConfigSchema } from './BigBedAdapter'
 import { configSchema as bedTabixAdapterConfigSchema } from './BedTabixAdapter'
+import { FileLocation } from '@jbrowse/core/util/types'
+import {
+  makeIndex,
+  makeIndexType,
+  AdapterGuesser,
+  getFileName,
+} from '@jbrowse/core/util/tracks'
 
 export default class BedPlugin extends Plugin {
   name = 'BedPlugin'
@@ -17,6 +24,28 @@ export default class BedPlugin extends Plugin {
             import('./BigBedAdapter/BigBedAdapter').then(r => r.default),
         }),
     )
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.(bb|bigbed)$/i
+          const adapterName = 'BigBedAdapter'
+          const fileName = getFileName(file)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bigBedLocation: file,
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
+
     pluginManager.addAdapterType(
       () =>
         new AdapterType({
@@ -26,5 +55,31 @@ export default class BedPlugin extends Plugin {
             import('./BedTabixAdapter/BedTabixAdapter').then(r => r.default),
         }),
     )
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.bed\.b?gz$/i
+          const adapterName = 'BedTabixAdapter'
+          const fileName = getFileName(file)
+          const indexName = index && getFileName(index)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bedGzLocation: file,
+              index: {
+                location: index || makeIndex(file, '.tbi'),
+                indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+              },
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
   }
 }