@jbrowse/plugin-alignments 1.5.1 → 1.5.5

package/src/index.ts

@@ -1,49 +1,21 @@
-import { lazy } from 'react'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import {
-  createBaseTrackConfig,
-  createBaseTrackModel,
-} from '@jbrowse/core/pluggableElementTypes/models'
 import { FileLocation } from '@jbrowse/core/util/types'
-import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
-import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'
-import { LinearWiggleDisplayReactComponent } from '@jbrowse/plugin-wiggle'
-import {
-  configSchema as alignmentsFeatureDetailConfigSchema,
-  stateModelFactory as alignmentsFeatureDetailStateModelFactory,
-} from './AlignmentsFeatureDetail'
-import BamAdapterF from './BamAdapter'
 import * as MismatchParser from './BamAdapter/MismatchParser'
-import CramAdapterF from './CramAdapter'
-import HtsgetBamAdapterF from './HtsgetBamAdapter'
-import {
-  configSchemaFactory as linearAligmentsDisplayConfigSchemaFactory,
-  modelFactory as linearAlignmentsDisplayModelFactory,
-  ReactComponent as LinearAlignmentsDisplayReactComponent,
-} from './LinearAlignmentsDisplay'
-import {
-  configSchemaFactory as linearPileupDisplayConfigSchemaFactory,
-  modelFactory as linearPileupDisplayModelFactory,
-} from './LinearPileupDisplay'
 import { LinearPileupDisplayModel } from './LinearPileupDisplay/model'
-import {
-  configSchemaFactory as linearSNPCoverageDisplayConfigSchemaFactory,
-  modelFactory as linearSNPCoverageDisplayModelFactory,
-} from './LinearSNPCoverageDisplay'
-import PileupRenderer, {
-  configSchema as pileupRendererConfigSchema,
-  ReactComponent as PileupRendererReactComponent,
-} from './PileupRenderer'
+
+import BamAdapterF from './CramAdapter'
+import CramAdapterF from './BamAdapter'
+import HtsgetBamAdapterF from './HtsgetBamAdapter'
 import SNPCoverageAdapterF from './SNPCoverageAdapter'
-import SNPCoverageRenderer, {
-  configSchema as SNPCoverageRendererConfigSchema,
-  ReactComponent as SNPCoverageRendererReactComponent,
-} from './SNPCoverageRenderer'
+import SNPCoverageRendererF from './SNPCoverageRenderer'
+import PileupRendererF from './PileupRenderer'
+import LinearAlignmentsDisplayF from './LinearAlignmentsDisplay'
+import LinearSNPCoverageDisplayF from './LinearSNPCoverageDisplay'
+import LinearPileupDisplayF from './LinearPileupDisplay'
+import AlignmentsTrackF from './AlignmentsTrack'
+import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail'
+
 import {
   PileupGetGlobalValueForTag,
   PileupGetVisibleModifications,
@@ -51,8 +23,8 @@ import {
 import {
   makeIndex,
   makeIndexType,
-  AdapterGuesser,
   getFileName,
+  AdapterGuesser,
   TrackTypeGuesser,
 } from '@jbrowse/core/util/tracks'
 
@@ -63,93 +35,19 @@ export default class AlignmentsPlugin extends Plugin {
   name = 'AlignmentsPlugin'
 
   install(pluginManager: PluginManager) {
-    pluginManager.addTrackType(() => {
-      const configSchema = ConfigurationSchema(
-        'AlignmentsTrack',
-        {},
-        { baseConfiguration: createBaseTrackConfig(pluginManager) },
-      )
-      const track = new TrackType({
-        name: 'AlignmentsTrack',
-        configSchema,
-        stateModel: createBaseTrackModel(
-          pluginManager,
-          'AlignmentsTrack',
-          configSchema,
-        ),
-      })
-      const linearAlignmentsDisplay = pluginManager.getDisplayType(
-        'LinearAlignmentsDisplay',
-      )
-      // Add LinearAlignmentsDisplay here so that it has priority over the other
-      // linear displays (defaults to order the displays are added, but we have
-      // to add the Pileup and SNPCoverage displays first).
-      track.addDisplayType(linearAlignmentsDisplay)
-      return track
-    })
-    pluginManager.addDisplayType(() => {
-      const configSchema = linearPileupDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearPileupDisplay',
-        configSchema,
-        stateModel: linearPileupDisplayModelFactory(
-          pluginManager,
-          configSchema,
-        ),
-        trackType: 'AlignmentsTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: BaseLinearDisplayComponent,
-      })
-    })
-    pluginManager.addDisplayType(() => {
-      const configSchema =
-        linearSNPCoverageDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearSNPCoverageDisplay',
-        configSchema,
-        stateModel: linearSNPCoverageDisplayModelFactory(
-          pluginManager,
-          configSchema,
-        ),
-        trackType: 'AlignmentsTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: LinearWiggleDisplayReactComponent,
-      })
-    })
-    pluginManager.addDisplayType(() => {
-      const configSchema =
-        linearAligmentsDisplayConfigSchemaFactory(pluginManager)
-      return new DisplayType({
-        name: 'LinearAlignmentsDisplay',
-        configSchema,
-        stateModel: linearAlignmentsDisplayModelFactory(
-          pluginManager,
-          configSchema,
-        ),
-        trackType: 'AlignmentsTrack',
-        viewType: 'LinearGenomeView',
-        ReactComponent: LinearAlignmentsDisplayReactComponent,
-      })
-    })
-    pluginManager.addWidgetType(
-      () =>
-        new WidgetType({
-          name: 'AlignmentsFeatureWidget',
-          heading: 'Feature details',
-          configSchema: alignmentsFeatureDetailConfigSchema,
-          stateModel: alignmentsFeatureDetailStateModelFactory(pluginManager),
-          ReactComponent: lazy(
-            () => import('./AlignmentsFeatureDetail/AlignmentsFeatureDetail'),
-          ),
-        }),
-    )
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'BamAdapter',
-          ...pluginManager.load(BamAdapterF),
-        }),
-    )
+    ;[
+      CramAdapterF,
+      BamAdapterF,
+      LinearPileupDisplayF,
+      LinearSNPCoverageDisplayF,
+      AlignmentsTrackF,
+      SNPCoverageAdapterF,
+      HtsgetBamAdapterF,
+      PileupRendererF,
+      SNPCoverageRendererF,
+      LinearAlignmentsDisplayF,
+      AlignmentsFeatureWidgetF,
+    ].map(f => f(pluginManager))
 
     pluginManager.addToExtensionPoint(
       'Core-guessAdapterForLocation',
@@ -159,56 +57,21 @@ export default class AlignmentsPlugin extends Plugin {
           index?: FileLocation,
           adapterHint?: string,
         ) => {
-          const regexGuess = /\.bam$/i
-          const adapterName = 'BamAdapter'
+          const regexGuess = /\.cram$/i
+          const adapterName = 'CramAdapter'
           const fileName = getFileName(file)
-          const indexName = index && getFileName(index)
           if (regexGuess.test(fileName) || adapterHint === adapterName) {
             return {
               type: adapterName,
-              bamLocation: file,
-              index: {
-                location: index || makeIndex(file, '.bai'),
-                indexType: makeIndexType(indexName, 'CSI', 'BAI'),
-              },
+              cramLocation: file,
+              craiLocation: index || makeIndex(file, '.crai'),
             }
           }
           return adapterGuesser(file, index, adapterHint)
         }
       },
     )
-    pluginManager.addToExtensionPoint(
-      'Core-guessTrackTypeForLocation',
-      (trackTypeGuesser: TrackTypeGuesser) => {
-        return (adapterName: string) => {
-          if (adapterName === 'BamAdapter') {
-            return 'AlignmentsTrack'
-          }
-          return trackTypeGuesser(adapterName)
-        }
-      },
-    )
 
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'SNPCoverageAdapter',
-          adapterMetadata: {
-            category: null,
-            displayName: null,
-            hiddenFromGUI: true,
-            description: null,
-          },
-          ...pluginManager.load(SNPCoverageAdapterF),
-        }),
-    )
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'CramAdapter',
-          ...pluginManager.load(CramAdapterF),
-        }),
-    )
     pluginManager.addToExtensionPoint(
       'Core-guessAdapterForLocation',
       (adapterGuesser: AdapterGuesser) => {
@@ -217,14 +80,18 @@ export default class AlignmentsPlugin extends Plugin {
           index?: FileLocation,
           adapterHint?: string,
         ) => {
-          const regexGuess = /\.cram$/i
-          const adapterName = 'CramAdapter'
+          const regexGuess = /\.bam$/i
+          const adapterName = 'BamAdapter'
           const fileName = getFileName(file)
+          const indexName = index && getFileName(index)
           if (regexGuess.test(fileName) || adapterHint === adapterName) {
             return {
               type: adapterName,
-              cramLocation: file,
-              craiLocation: index || makeIndex(file, '.crai'),
+              bamLocation: file,
+              index: {
+                location: index || makeIndex(file, '.bai'),
+                indexType: makeIndexType(indexName, 'CSI', 'BAI'),
+              },
             }
           }
           return adapterGuesser(file, index, adapterHint)
@@ -235,7 +102,7 @@ export default class AlignmentsPlugin extends Plugin {
       'Core-guessTrackTypeForLocation',
       (trackTypeGuesser: TrackTypeGuesser) => {
         return (adapterName: string) => {
-          if (adapterName === 'CramAdapter') {
+          if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
             return 'AlignmentsTrack'
           }
           return trackTypeGuesser(adapterName)
@@ -243,38 +110,6 @@ export default class AlignmentsPlugin extends Plugin {
       },
     )
 
-    pluginManager.addAdapterType(
-      () =>
-        new AdapterType({
-          name: 'HtsgetBamAdapter',
-          adapterMetadata: {
-            category: null,
-            hiddenFromGUI: true,
-            displayName: null,
-            description: null,
-          },
-          ...pluginManager.load(HtsgetBamAdapterF),
-        }),
-    )
-    pluginManager.addRendererType(
-      () =>
-        new PileupRenderer({
-          name: 'PileupRenderer',
-          ReactComponent: PileupRendererReactComponent,
-          configSchema: pileupRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-    pluginManager.addRendererType(
-      () =>
-        new SNPCoverageRenderer({
-          name: 'SNPCoverageRenderer',
-          ReactComponent: SNPCoverageRendererReactComponent,
-          configSchema: SNPCoverageRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-
     pluginManager.addRpcMethod(
       () => new PileupGetGlobalValueForTag(pluginManager),
     )

package/src/SNPCoverageAdapter/SNPCoverageAdapter.test.ts

@@ -1,275 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { LocalFile } from 'generic-filehandle'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { SnapshotIn } from 'mobx-state-tree'
-import AdapterF from './index'
-import CramAdapterF from '../CramAdapter'
-import BamAdapterF from '../BamAdapter'
-
-import { SequenceAdapter } from '../CramAdapter/CramTestAdapters'
-
-const pluginManager = new PluginManager()
-const { getAdapterClass: getSNPCoverageAdapter, configSchema } =
-  pluginManager.load(AdapterF)
-const { getAdapterClass: getCramAdapter, configSchema: CramConfigSchema } =
-  pluginManager.load(CramAdapterF)
-const { getAdapterClass: getBamAdapter, configSchema: BamConfigSchema } =
-  pluginManager.load(BamAdapterF)
-
-pluginManager.configure()
-
-async function newSNPCoverageWithBam(
-  bamConf: SnapshotIn<typeof BamConfigSchema>,
-) {
-  const BamAdapter = await getBamAdapter()
-  const SNPCoverageAdapter = await getSNPCoverageAdapter()
-  return new SNPCoverageAdapter(configSchema.create({}), async () => {
-    return {
-      dataAdapter: new BamAdapter(BamConfigSchema.create(bamConf)),
-      sessionIds: new Set(),
-    }
-  })
-}
-
-test('SNP adapter can fetch features from volvox.bam using bam subadapter', async () => {
-  const adapter = await newSNPCoverageWithBam({
-    type: 'BamAdapter',
-    bamLocation: {
-      localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-      locationType: 'LocalPathLocation',
-    },
-    index: {
-      location: {
-        localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
-        locationType: 'LocalPathLocation',
-      },
-      indexType: 'BAI',
-    },
-  })
-
-  const features = adapter.getFeatures(
-    {
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 20000,
-    },
-    {
-      bpPerPx: 0.2,
-    },
-  )
-
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  expect(featuresArray[0].get('refName')).toBe('ctgA')
-  expect(featuresArray[0].get('snpinfo')).toBeTruthy()
-
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.length).toEqual(19998)
-  expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot()
-
-  expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-})
-
-test('test usage of BamSlightlyLazyFeature toJSON in a SNP adapter', async () => {
-  const adapter = await newSNPCoverageWithBam({
-    type: 'BamAdapter',
-    bamLocation: {
-      localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-      locationType: 'LocalPathLocation',
-    },
-    index: {
-      location: {
-        localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
-        locationType: 'LocalPathLocation',
-      },
-      indexType: 'BAI',
-    },
-  })
-
-  const features = adapter.getFeatures({
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 100,
-  })
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  const f = featuresArray[0].toJSON()
-
-  expect(f.refName).toBe('ctgA')
-  expect(f.start).toBe(2)
-  expect(f.end).toBe(3)
-  expect(f.snpinfo).toBeTruthy()
-})
-
-test('test usage of getMultiRegion stats, SNP adapter can generate a domain from BamFile', async () => {
-  const adapter = await newSNPCoverageWithBam({
-    type: 'BamAdapter',
-    bamLocation: {
-      localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-      locationType: 'LocalPathLocation',
-    },
-    index: {
-      location: {
-        localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
-        locationType: 'LocalPathLocation',
-      },
-      indexType: 'BAI',
-    },
-  })
-
-  const stats = await adapter.getMultiRegionStats(
-    [
-      {
-        assemblyName: 'volvox',
-        refName: 'ctgA',
-        start: 0,
-        end: 100,
-      },
-    ],
-    {
-      opts: {
-        signal: {
-          aborted: false,
-          onabort: null,
-        },
-        bpPerPx: 0.2,
-      },
-    },
-  )
-
-  expect(Object.keys(stats).length).toEqual(9)
-  expect(stats.scoreMin).toEqual(1)
-  expect(stats.scoreMax).toEqual(13)
-})
-
-async function newSNPCoverageWithCram(
-  cramConf: SnapshotIn<typeof CramConfigSchema>,
-  sequenceFileName: string,
-) {
-  const CramAdapter = await getCramAdapter()
-  const SNPCoverageAdapter = await getSNPCoverageAdapter()
-  return new SNPCoverageAdapter(configSchema.create({}), async () => {
-    return {
-      dataAdapter: new CramAdapter(
-        CramConfigSchema.create(cramConf),
-        async () => {
-          return {
-            dataAdapter: new SequenceAdapter(new LocalFile(sequenceFileName)),
-            sessionIds: new Set(),
-          }
-        },
-      ),
-      sessionIds: new Set(),
-    }
-  })
-}
-
-test('SNP adapter can fetch features from volvox.cram using cram subadapter', async () => {
-  const adapter = await newSNPCoverageWithCram(
-    {
-      type: 'CramAdapter',
-      cramLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-        locationType: 'LocalPathLocation',
-      },
-      craiLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-        locationType: 'LocalPathLocation',
-      },
-    },
-    require.resolve('../../test_data/volvox.fa'),
-  )
-
-  const features = adapter.getFeatures(
-    {
-      assemblyName: 'volvox',
-      refName: 'ctgA',
-      start: 0,
-      end: 20000,
-    },
-    {
-      bpPerPx: 0.2,
-    },
-  )
-
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  expect(featuresArray[0].get('refName')).toBe('ctgA')
-  expect(featuresArray[0].get('snpinfo')).toBeTruthy()
-
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.length).toEqual(19998)
-  expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot()
-  expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-})
-
-test('test usage of CramSlightlyLazyFeature toJSON in a SNP adapter', async () => {
-  const adapter = await newSNPCoverageWithCram(
-    {
-      type: 'CramAdapter',
-      cramLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-        locationType: 'LocalPathLocation',
-      },
-      craiLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-        locationType: 'LocalPathLocation',
-      },
-    },
-    require.resolve('../../test_data/volvox.fa'),
-  )
-
-  const features = adapter.getFeatures({
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 100,
-  })
-  const featuresArray = await features.pipe(toArray()).toPromise()
-  const f = featuresArray[0].toJSON()
-
-  expect(f.refName).toBe('ctgA')
-  expect(f.start).toBe(2)
-  expect(f.end).toBe(3)
-  expect(f.snpinfo).toBeTruthy()
-})
-
-test('test usage of getMultiRegion stats, SNP adapter can generate a domain from CramFile', async () => {
-  const adapter = await newSNPCoverageWithCram(
-    {
-      type: 'CramAdapter',
-      cramLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram'),
-        locationType: 'LocalPathLocation',
-      },
-      craiLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.cram.crai'),
-        locationType: 'LocalPathLocation',
-      },
-    },
-    require.resolve('../../test_data/volvox.fa'),
-  )
-
-  const stats = await adapter.getMultiRegionStats(
-    [
-      {
-        assemblyName: 'volvox',
-        refName: 'ctgA',
-        start: 0,
-        end: 100,
-      },
-    ],
-    {
-      opts: {
-        signal: {
-          aborted: false,
-          onabort: null,
-        },
-        bpPerPx: 0.2,
-      },
-    },
-  )
-
-  expect(Object.keys(stats).length).toEqual(9)
-  expect(stats.scoreMin).toEqual(1)
-  expect(stats.scoreMax).toEqual(13)
-})