@jbrowse/plugin-variants 2.6.1 → 2.6.2

package/src/extensionPoints.ts

@@ -1,74 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { FileLocation } from '@jbrowse/core/util/types'
-import {
-  makeIndex,
-  makeIndexType,
-  getFileName,
-  AdapterGuesser,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.vcf\.b?gz$/i
-        const adapterName = 'VcfTabixAdapter'
-        const fileName = getFileName(file)
-        const indexName = index && getFileName(index)
-        const obj = {
-          type: adapterName,
-          vcfGzLocation: file,
-          index: {
-            location: index || makeIndex(file, '.tbi'),
-            indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-          },
-        }
-        if (regexGuess.test(fileName) && !adapterHint) {
-          return obj
-        } else if (adapterHint === adapterName) {
-          return obj
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-  pluginManager.addToExtensionPoint(
-    'Core-guessTrackTypeForLocation',
-    (trackTypeGuesser: TrackTypeGuesser) => {
-      return (adapterName: string) => {
-        if (adapterName === 'VcfTabixAdapter' || adapterName === 'VcfAdapter') {
-          return 'VariantTrack'
-        }
-        return trackTypeGuesser(adapterName)
-      }
-    },
-  )
-
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.vcf$/i
-        const adapterName = 'VcfAdapter'
-        const fileName = getFileName(file)
-        if (regexGuess.test(fileName) || adapterHint === adapterName) {
-          return {
-            type: adapterName,
-            vcfLocation: file,
-          }
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-}

package/src/index.test.ts

@@ -1,32 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import Alignments from '@jbrowse/plugin-alignments'
-import SVG from '@jbrowse/plugin-svg'
-import { getSnapshot } from 'mobx-state-tree'
-import ThisPlugin from '.'
-
-test('plugin in a stock JBrowse', () => {
-  const pluginManager = new PluginManager([
-    new ThisPlugin(),
-    new Alignments(),
-    new SVG(),
-  ])
-  pluginManager.createPluggableElements()
-  pluginManager.configure()
-  expect(() => pluginManager.addPlugin(new ThisPlugin())).toThrow(
-    /JBrowse already configured, cannot add plugins/,
-  )
-
-  const VcfTabixAdapter = pluginManager.getAdapterType('VcfTabixAdapter')
-  const config = VcfTabixAdapter.configSchema.create({
-    type: 'VcfTabixAdapter',
-  })
-  expect(getSnapshot(config)).toMatchSnapshot()
-
-  const VariantTrack = pluginManager.getTrackType('VariantTrack')
-  const config2 = VariantTrack.configSchema.create({
-    type: 'VariantTrack',
-    trackId: 'trackId0',
-    adapter: { type: 'VcfTabixAdapter' },
-  })
-  expect(getSnapshot(config2)).toMatchSnapshot()
-})

package/src/index.ts

@@ -1,27 +0,0 @@
-import VcfAdapterF from './VcfAdapter'
-import VcfTabixAdapterF from './VcfTabixAdapter'
-import ExtensionPointsF from './extensionPoints'
-import VariantTrackF from './VariantTrack'
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import ChordVariantDisplayF from './ChordVariantDisplay'
-import LinearVariantDisplayF from './LinearVariantDisplay'
-import StructuralVariantChordRendererF from './StructuralVariantChordRenderer'
-import VariantFeatureWidgetF from './VariantFeatureWidget'
-
-export default class VariantsPlugin extends Plugin {
-  name = 'VariantsPlugin'
-
-  install(pluginManager: PluginManager) {
-    VcfAdapterF(pluginManager)
-    VcfTabixAdapterF(pluginManager)
-    VariantFeatureWidgetF(pluginManager)
-    VariantTrackF(pluginManager)
-    ExtensionPointsF(pluginManager)
-    LinearVariantDisplayF(pluginManager)
-    StructuralVariantChordRendererF(pluginManager)
-    ChordVariantDisplayF(pluginManager)
-  }
-}
-
-export { default as VcfFeature } from './VcfFeature'