@jbrowse/plugin-variants 1.4.3 → 1.5.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "1.4.3",
+  "version": "1.5.2",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -35,12 +35,13 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^1.3.4",
-    "@gmod/tabix": "^1.5.0",
-    "@gmod/vcf": "^5.0.0",
-    "@material-ui/data-grid": "^4.0.0-alpha.37",
+    "@flatten-js/interval-tree": "^1.0.14",
+    "@gmod/bgzf-filehandle": "^1.4.1",
+    "@gmod/tabix": "^1.5.2",
+    "@gmod/vcf": "^5.0.3",
     "@material-ui/icons": "^4.11.2",
-    "generic-filehandle": "^2.0.0"
+    "@mui/x-data-grid": "^4.0.1",
+    "generic-filehandle": "^2.2.2"
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
@@ -57,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "99db07eaad1b00387768ba1e1f31f917c3aad9cf"
+  "gitHead": "94fdfbc34787ab8f12a87e00038da74b247b42fa"
 }

package/src/LinearVariantDisplay/configSchema.test.js

@@ -1,10 +1,7 @@
 import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import PileupRenderer, {
-  configSchema as pileupRendererConfigSchema,
-  ReactComponent as PileupRendererReactComponent,
-} from '@jbrowse/plugin-alignments/src/PileupRenderer'
+import PileupRenderer from '@jbrowse/plugin-alignments/src/PileupRenderer'
 import {
   configSchema as svgFeatureRendererConfigSchema,
   ReactComponent as SvgFeatureRendererReactComponent,
@@ -22,15 +19,7 @@ afterEach(() => {
 
 class PileupRendererPlugin extends Plugin {
   install(pluginManager) {
-    pluginManager.addRendererType(
-      () =>
-        new PileupRenderer({
-          name: 'PileupRenderer',
-          ReactComponent: PileupRendererReactComponent,
-          configSchema: pileupRendererConfigSchema,
-          pluginManager,
-        }),
-    )
+    PileupRenderer(pluginManager)
   }
 }
 

package/src/LinearVariantDisplay/configSchema.ts

@@ -18,4 +18,5 @@ export function LinearVariantDisplayConfigFactory(
 export type LinearVariantDisplayConfigModel = ReturnType<
   typeof LinearVariantDisplayConfigFactory
 >
-export type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>
+export type LinearVariantDisplayConfig =
+  Instance<LinearVariantDisplayConfigModel>

package/src/StructuralVariantChordRenderer/ReactComponent.js

@@ -37,7 +37,7 @@ const Chord = observer(function Chord({
   let endPosition
   let endBlock
   const alt = feature.get('ALT')?.[0]
-  const bnd = parseBreakend(alt)
+  const bnd = alt && parseBreakend(alt)
   if (bnd) {
     // VCF BND
     const matePosition = bnd.MatePosition.split(':')
@@ -92,6 +92,7 @@ const Chord = observer(function Chord({
         onMouseOut={evt => {
           if (!selected) {
             evt.target.style.stroke = strokeColor
+            evt.target.style.strokeWidth = 1
           }
         }}
       />

package/src/VariantFeatureWidget/VariantFeatureWidget.tsx

@@ -12,7 +12,7 @@ import {
 import SimpleFeature, {
   SimpleFeatureSerialized,
 } from '@jbrowse/core/util/simpleFeature'
-import { DataGrid } from '@material-ui/data-grid'
+import { DataGrid } from '@mui/x-data-grid'
 import { observer } from 'mobx-react'
 import { getSession } from '@jbrowse/core/util'
 import { getEnv } from 'mobx-state-tree'
@@ -204,14 +204,10 @@ function VariantFeatureDetails(props: any) {
   const { samples, ...rest } = feat
   const basicDescriptions = {
     CHROM: 'chromosome: An identifier from the reference genome',
-    POS:
-      'position: The reference position, with the 1st base having position 1',
-    ID:
-      'identifier: Semi-colon separated list of unique identifiers where available',
-    REF:
-      'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
-    ALT:
-      'alternate base(s): Comma-separated list of alternate non-reference alleles',
+    POS: 'position: The reference position, with the 1st base having position 1',
+    ID: 'identifier: Semi-colon separated list of unique identifiers where available',
+    REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',
+    ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',
     QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',
     FILTER:
       'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',

package/src/VcfAdapter/VcfAdapter.test.ts

@@ -9,6 +9,7 @@ test('adapter can fetch variants from volvox.vcf', async () => {
     configSchema.create({
       vcfLocation: {
         localPath: require.resolve('./test_data/volvox.filtered.vcf'),
+        locationType: 'LocalPathLocation',
       },
     }),
   )

package/src/VcfAdapter/VcfAdapter.ts

@@ -2,116 +2,123 @@ import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { FileLocation, Region } from '@jbrowse/core/util/types'
+import { Region } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { Feature } from '@jbrowse/core/util/simpleFeature'
 import { readConfObject } from '@jbrowse/core/configuration'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
-import VcfFeature from '../VcfTabixAdapter/VcfFeature'
-import VCF from '@gmod/vcf'
+import IntervalTree from '@flatten-js/interval-tree'
 import { unzip } from '@gmod/bgzf-filehandle'
+import VCF from '@gmod/vcf'
+import VcfFeature from '../VcfTabixAdapter/VcfFeature'
 
 const readVcf = (f: string) => {
   const lines = f.split('\n')
   const header: string[] = []
-  const refNames: string[] = []
   const rest: string[] = []
   lines.forEach(line => {
-    if (line.startsWith('##contig')) {
-      refNames.push(line.split('##contig=<ID=')[1].split(',')[0])
-    } else if (line.startsWith('#')) {
+    if (line.startsWith('#')) {
       header.push(line)
     } else if (line) {
       rest.push(line)
     }
   })
-  return { header: header.join('\n'), lines: rest, refNames }
+  return { header: header.join('\n'), lines: rest }
+}
+
+function isGzip(buf: Buffer) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
 }
 
 export default class VcfAdapter extends BaseFeatureDataAdapter {
   public static capabilities = ['getFeatures', 'getRefNames']
 
-  private setupP?: Promise<Feature[]>
-
-  public constructor(config: AnyConfigurationModel) {
-    super(config)
-  }
-
-  private async decodeFileContents() {
-    const vcfLocation = readConfObject(
-      this.config,
-      'vcfLocation',
-    ) as FileLocation
-
-    let fileContents = await openLocation(vcfLocation).readFile()
-
-    if (
-      typeof fileContents[0] === 'number' &&
-      fileContents[0] === 31 &&
-      typeof fileContents[1] === 'number' &&
-      fileContents[1] === 139 &&
-      typeof fileContents[2] === 'number' &&
-      fileContents[2] === 8
-    ) {
-      fileContents = new TextDecoder().decode(await unzip(fileContents))
-    } else {
-      fileContents = fileContents.toString()
-    }
-
-    return readVcf(fileContents)
-  }
+  protected vcfFeatures?: Promise<{
+    header: string
+    intervalTree: Record<string, IntervalTree>
+  }>
 
   public async getHeader() {
-    const { header } = await this.decodeFileContents()
+    const { header } = await this.setup()
     return header
   }
 
   async getMetadata() {
-    const { header } = await this.decodeFileContents()
+    const { header } = await this.setup()
     const parser = new VCF({ header: header })
     return parser.getMetadata()
   }
 
-  public async getLines() {
-    const { header, lines } = await this.decodeFileContents()
+  // converts lines into an interval tree
+  public async setupP() {
+    const buffer = await openLocation(
+      readConfObject(this.config, 'vcfLocation'),
+      this.pluginManager,
+    ).readFile()
 
-    const parser = new VCF({ header: header })
+    const buf = isGzip(buffer as Buffer) ? await unzip(buffer) : buffer
+
+    // 512MB  max chrome string length is 512MB
+    if (buf.length > 536_870_888) {
+      throw new Error('Data exceeds maximum string length (512MB)')
+    }
+
+    const str = new TextDecoder().decode(buf)
+    const { header, lines } = readVcf(str)
 
-    return lines.map((line, index) => {
-      return new VcfFeature({
-        variant: parser.parseLine(line),
-        parser,
-        id: `${this.id}-vcf-${index}`,
+    const intervalTree = lines
+      .map((line, id) => {
+        const [refName, startP, , ref, , , , info] = line.split('\t')
+        const start = +startP - 1
+        const end = +(info.match(/END=(\d+)/)?.[1].trim() || start + ref.length)
+        return { line, refName, start, end, id }
       })
-    })
+      .reduce((acc, obj) => {
+        const key = obj.refName
+        if (!acc[key]) {
+          acc[key] = new IntervalTree()
+        }
+        acc[key].insert([obj.start, obj.end], obj)
+        return acc
+      }, {} as Record<string, IntervalTree>)
+
+    return { header, intervalTree }
   }
 
   public async setup() {
-    if (!this.setupP) {
-      this.setupP = this.getLines()
+    if (!this.vcfFeatures) {
+      this.vcfFeatures = this.setupP().catch(e => {
+        this.vcfFeatures = undefined
+        throw e
+      })
     }
-    return this.setupP
+    return this.vcfFeatures
   }
 
   public async getRefNames(_: BaseOptions = {}) {
-    const { refNames } = await this.decodeFileContents()
-    return refNames
+    const { intervalTree } = await this.setup()
+    return Object.keys(intervalTree)
   }
 
   public getFeatures(region: Region, opts: BaseOptions = {}) {
     return ObservableCreate<Feature>(async observer => {
-      const feats = await this.setup()
-      feats.forEach(f => {
-        if (
-          f.get('refName') === region.refName &&
-          f.get('end') > region.start &&
-          f.get('start') < region.end
-        ) {
-          observer.next(f)
-        }
-      })
-      observer.complete()
+      try {
+        const { start, end, refName } = region
+        const { header, intervalTree } = await this.setup()
+        const parser = new VCF({ header: header })
+        intervalTree[refName]?.search([start, end]).forEach(f =>
+          observer.next(
+            new VcfFeature({
+              variant: parser.parseLine(f.line),
+              parser,
+              id: `${this.id}-${f.id}`,
+            }),
+          ),
+        )
+        observer.complete()
+      } catch (e) {
+        observer.error(e)
+      }
     }, opts.signal)
   }
 

package/src/VcfAdapter/__snapshots__/VcfAdapter.test.ts.snap

@@ -66,7 +66,7 @@ Array [
     },
     "start": 276,
     "type": "SNV",
-    "uniqueId": "test-vcf-0",
+    "uniqueId": "test-0",
   },
   Object {
     "ALT": Array [
@@ -132,7 +132,7 @@ Array [
     },
     "start": 1693,
     "type": "SNV",
-    "uniqueId": "test-vcf-1",
+    "uniqueId": "test-1",
   },
   Object {
     "ALT": Array [
@@ -198,7 +198,7 @@ Array [
     },
     "start": 2643,
     "type": "SNV",
-    "uniqueId": "test-vcf-2",
+    "uniqueId": "test-2",
   },
   Object {
     "ALT": Array [
@@ -258,7 +258,7 @@ Array [
     },
     "start": 3212,
     "type": "SNV",
-    "uniqueId": "test-vcf-3",
+    "uniqueId": "test-3",
   },
   Object {
     "ALT": Array [
@@ -319,7 +319,7 @@ Array [
     },
     "start": 3857,
     "type": "deletion",
-    "uniqueId": "test-vcf-4",
+    "uniqueId": "test-4",
   },
 ]
 `;

package/src/VcfAdapter/configSchema.ts

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

package/src/VcfTabixAdapter/VcfTabixAdapter.test.ts

@@ -7,11 +7,13 @@ test('adapter can fetch variants from volvox.vcf.gz', async () => {
     configSchema.create({
       vcfGzLocation: {
         localPath: require.resolve('./test_data/volvox.filtered.vcf.gz'),
+        locationType: 'LocalPathLocation',
       },
       index: {
         indexType: 'TBI',
         location: {
           localPath: require.resolve('./test_data/volvox.filtered.vcf.gz.tbi'),
+          locationType: 'LocalPathLocation',
         },
       },
     }),
@@ -21,11 +23,13 @@ test('adapter can fetch variants from volvox.vcf.gz', async () => {
     configSchema.create({
       vcfGzLocation: {
         localPath: require.resolve('./test_data/volvox.filtered.vcf.gz'),
+        locationType: 'LocalPathLocation',
       },
       index: {
         indexType: 'CSI',
         location: {
           localPath: require.resolve('./test_data/volvox.filtered.vcf.gz.csi'),
+          locationType: 'LocalPathLocation',
         },
       },
     }),

package/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -30,12 +30,19 @@ export default class extends BaseFeatureDataAdapter {
       const location = readConfObject(this.config, ['index', 'location'])
       const indexType = readConfObject(this.config, ['index', 'indexType'])
 
-      const filehandle = openLocation(vcfGzLocation as FileLocation)
+      const filehandle = openLocation(
+        vcfGzLocation as FileLocation,
+        this.pluginManager,
+      )
       const isCSI = indexType === 'CSI'
       const vcf = new TabixIndexedFile({
         filehandle,
-        csiFilehandle: isCSI ? openLocation(location) : undefined,
-        tbiFilehandle: !isCSI ? openLocation(location) : undefined,
+        csiFilehandle: isCSI
+          ? openLocation(location, this.pluginManager)
+          : undefined,
+        tbiFilehandle: !isCSI
+          ? openLocation(location, this.pluginManager)
+          : undefined,
         chunkCacheSize: 50 * 2 ** 20,
         chunkSizeLimit: 1000000000,
       })

package/src/VcfTabixAdapter/configSchema.ts

@@ -6,7 +6,7 @@ export default ConfigurationSchema(
   {
     vcfGzLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.vcf.gz' },
+      defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
     },
     index: ConfigurationSchema('VcfIndex', {
       indexType: {
@@ -16,7 +16,10 @@ export default ConfigurationSchema(
       },
       location: {
         type: 'fileLocation',
-        defaultValue: { uri: '/path/to/my.vcf.gz.tbi' },
+        defaultValue: {
+          uri: '/path/to/my.vcf.gz.tbi',
+          locationType: 'UriLocation',
+        },
       },
     }),
   },

package/src/index.ts

@@ -6,6 +6,7 @@ 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'
@@ -23,6 +24,13 @@ import {
 } from './VariantFeatureWidget'
 import { configSchema as vcfTabixAdapterConfigSchema } from './VcfTabixAdapter'
 import { configSchema as vcfAdapterConfigSchema } from './VcfAdapter'
+import {
+  makeIndex,
+  makeIndexType,
+  AdapterGuesser,
+  getFileName,
+  TrackTypeGuesser,
+} from '@jbrowse/core/util/tracks'
 
 export default class VariantsPlugin extends Plugin {
   name = 'VariantsPlugin'
@@ -37,6 +45,43 @@ export default class VariantsPlugin extends Plugin {
             import('./VcfTabixAdapter/VcfTabixAdapter').then(r => r.default),
         }),
     )
+    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)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              vcfGzLocation: file,
+              index: {
+                location: index || makeIndex(file, '.tbi'),
+                indexType: makeIndexType(indexName, 'CSI', 'TBI'),
+              },
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
+    pluginManager.addToExtensionPoint(
+      'Core-guessTrackTypeForLocation',
+      (trackTypeGuesser: TrackTypeGuesser) => {
+        return (adapterName: string) => {
+          if (adapterName === 'VcfTabixAdapter') {
+            return 'VariantTrack'
+          }
+          return trackTypeGuesser(adapterName)
+        }
+      },
+    )
 
     pluginManager.addAdapterType(
       () =>
@@ -48,6 +93,28 @@ export default class VariantsPlugin extends Plugin {
         }),
     )
 
+    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)
+        }
+      },
+    )
+
     pluginManager.addRendererType(() =>
       pluginManager.jbrequire(StructuralVariantChordRendererFactory),
     )
@@ -73,9 +140,8 @@ export default class VariantsPlugin extends Plugin {
     )
 
     pluginManager.addDisplayType(() => {
-      const configSchema = linearVariantDisplayConfigSchemaFactory(
-        pluginManager,
-      )
+      const configSchema =
+        linearVariantDisplayConfigSchemaFactory(pluginManager)
       return new DisplayType({
         name: 'LinearVariantDisplay',
         configSchema,