@jbrowse/plugin-bed 2.2.1 → 2.3.0

package/src/BedpeAdapter/configSchema.ts

@@ -0,0 +1,34 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config BedpeAdapter
+ * intended for SVs in a single assembly
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const BedpeAdapter = ConfigurationSchema(
+  'BedpeAdapter',
+  {
+    /**
+     * #slot
+     * can be plaintext or gzipped, not indexed so loaded into memory on startup
+     */
+    bedpeLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/my.bedpe.gz',
+        locationType: 'UriLocation',
+      },
+    },
+    /**
+     * #slot
+     */
+    columnNames: {
+      type: 'stringArray',
+      description: 'List of column names',
+      defaultValue: [],
+    },
+  },
+  { explicitlyTyped: true },
+)
+export default BedpeAdapter

package/src/BedpeAdapter/index.ts

@@ -0,0 +1,16 @@
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+
+import configSchema from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'BedpeAdapter',
+        displayName: 'BEDPE adapter',
+        configSchema,
+        getAdapterClass: () => import('./BedpeAdapter').then(r => r.default),
+      }),
+  )
+}

package/src/BigBedAdapter/index.ts

@@ -1 +1,16 @@
-export { default as configSchema } from './configSchema'
+import PluginManager from '@jbrowse/core/PluginManager'
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
+
+import configSchema from './configSchema'
+
+export default (pluginManager: PluginManager) => {
+  pluginManager.addAdapterType(
+    () =>
+      new AdapterType({
+        name: 'BigBedAdapter',
+        displayName: 'BigBed adapter',
+        configSchema,
+        getAdapterClass: () => import('./BigBedAdapter').then(r => r.default),
+      }),
+  )
+}

package/src/index.ts

@@ -1,9 +1,9 @@
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
 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 { configSchema as bedAdapterConfigSchema } from './BedAdapter'
+import BigBedAdapterF from './BigBedAdapter'
+import BedpeAdapterF from './BedpeAdapter'
+import BedTabixAdapterF from './BedTabixAdapter'
+import BedAdapterF from './BedAdapter'
 import { FileLocation } from '@jbrowse/core/util/types'
 import {
   getFileName,
@@ -16,15 +16,10 @@ export default class BedPlugin extends Plugin {
   name = 'BedPlugin'
 
   install(pluginManager: PluginManager) {
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'BigBedAdapter',
-          configSchema: bigBedAdapterConfigSchema,
-          getAdapterClass: () =>
-            import('./BigBedAdapter/BigBedAdapter').then(r => r.default),
-        }),
-    )
+    BigBedAdapterF(pluginManager)
+    BedAdapterF(pluginManager)
+    BedpeAdapterF(pluginManager)
+    BedTabixAdapterF(pluginManager)
     pluginManager.addToExtensionPoint(
       'Core-guessAdapterForLocation',
       (adapterGuesser: AdapterGuesser) => {
@@ -51,25 +46,28 @@ export default class BedPlugin extends Plugin {
       },
     )
 
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'BedTabixAdapter',
-          configSchema: bedTabixAdapterConfigSchema,
-          getAdapterClass: () =>
-            import('./BedTabixAdapter/BedTabixAdapter').then(r => r.default),
-        }),
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.bedpe\.gz$/i
+          const adapterName = 'BedpeAdapter'
+          const fileName = getFileName(file)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bedpeLocation: file,
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
     )
 
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'BedAdapter',
-          configSchema: bedAdapterConfigSchema,
-          getAdapterClass: () =>
-            import('./BedAdapter/BedAdapter').then(r => r.default),
-        }),
-    )
     pluginManager.addToExtensionPoint(
       'Core-guessAdapterForLocation',
       (adapterGuesser: AdapterGuesser) => {