@jbrowse/plugin-variants 1.5.0 → 1.5.4

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "1.5.0",
+  "version": "1.5.4",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -35,13 +35,13 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@flatten-js/interval-tree": "^1.0.14",
-    "@gmod/bgzf-filehandle": "^1.3.4",
-    "@gmod/tabix": "^1.5.0",
-    "@gmod/vcf": "^5.0.0",
+    "@flatten-js/interval-tree": "^1.0.15",
+    "@gmod/bgzf-filehandle": "^1.4.2",
+    "@gmod/tabix": "^1.5.2",
+    "@gmod/vcf": "^5.0.4",
     "@material-ui/icons": "^4.11.2",
     "@mui/x-data-grid": "^4.0.1",
-    "generic-filehandle": "^2.2.0"
+    "generic-filehandle": "^2.2.2"
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "542025578a39bd170c8a166f2568ee7edbd54072"
+  "gitHead": "0c398214590969168694b4ed8e20b595178b9efd"
 }

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/VariantFeatureWidget/VariantFeatureWidget.tsx

@@ -225,7 +225,7 @@ function VariantFeatureDetails(props: any) {
         <BreakendPanel
           feature={feat}
           locStrings={feat.ALT.map(
-            (alt: string) => parseBreakend(alt).MatePosition,
+            (alt: string) => parseBreakend(alt)?.MatePosition || '',
           )}
           model={model}
         />

package/src/VariantFeatureWidget/__snapshots__/VariantFeatureWidget.test.js.snap

@@ -182,6 +182,7 @@ exports[`VariantTrack widget renders with just the required model elements 1`] =
               >
                 <div
                   class="makeStyles-fieldName"
+                  style="width: 62px;"
                 >
                   INFO.MQ
                 </div>

package/src/VcfAdapter/VcfAdapter.ts

@@ -2,135 +2,119 @@ 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 IntervalTree from '@flatten-js/interval-tree'
-import VcfFeature from '../VcfTabixAdapter/VcfFeature'
-import VCF from '@gmod/vcf'
 import { unzip } from '@gmod/bgzf-filehandle'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
+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']
 
-  protected vcfFeatures?: Promise<Record<string, IntervalTree>>
-
-  public constructor(
-    config: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-  }
-
-  private async decodeFileContents() {
-    const vcfLocation = readConfObject(
-      this.config,
-      'vcfLocation',
-    ) as FileLocation
-
-    let fileContents = await openLocation(
-      vcfLocation,
-      this.pluginManager,
-    ).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 buf = isGzip(buffer) ? await unzip(buffer) : buffer
 
-    const parser = new VCF({ header: header })
+    // 512MB  max chrome string length is 512MB
+    if (buf.length > 536_870_888) {
+      throw new Error('Data exceeds maximum string length (512MB)')
+    }
 
-    return lines.map((line, index) => {
-      return new VcfFeature({
-        variant: parser.parseLine(line),
-        parser,
-        id: `${this.id}-vcf-${index}`,
+    const str = new TextDecoder().decode(buf)
+    const { header, lines } = readVcf(str)
+
+    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.vcfFeatures) {
-      this.vcfFeatures = this.getLines().then(feats => {
-        return feats.reduce(
-          (acc: Record<string, IntervalTree>, obj: VcfFeature) => {
-            const key = obj.get('refName')
-            if (!acc[key]) {
-              acc[key] = new IntervalTree()
-            }
-            acc[key].insert([obj.get('start'), obj.get('end')], obj)
-            return acc
-          },
-          {},
-        )
+      this.vcfFeatures = this.setupP().catch(e => {
+        this.vcfFeatures = undefined
+        throw e
       })
     }
     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 => {
       try {
         const { start, end, refName } = region
-        const vcfFeatures = await this.setup()
-        const tree = vcfFeatures[refName]
-        const feats = tree.search([start, end]) //  expected array ['val1']
-        feats.forEach(f => {
-          observer.next(f)
-        })
+        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)

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/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -20,7 +20,7 @@ import VcfFeature from './VcfFeature'
 export default class extends BaseFeatureDataAdapter {
   protected configured?: Promise<{
     vcf: TabixIndexedFile
-    parser: typeof VcfParser
+    parser: VcfParser
     filehandle: GenericFilehandle
   }>
 

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),
     )

package/src/declare.d.ts

@@ -1,2 +0,0 @@
-declare module '@gmod/vcf'
-declare module '@gmod/bgzf-filehandle'