Add BEDPE adapter type

plugins/bed/src/BedAdapter/index.ts

@@ -1 +1,15 @@
-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: 'BedAdapter',
+        configSchema,
+        getAdapterClass: () => import('./BedAdapter').then(r => r.default),
+      }),
+  )
+}

plugins/bed/src/BedTabixAdapter/index.ts

@@ -1 +1,15 @@
-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: 'BedTabixAdapter',
+        configSchema,
+        getAdapterClass: () => import('./BedTabixAdapter').then(r => r.default),
+      }),
+  )
+}

plugins/bed/src/BedpeAdapter/BedpeAdapter.ts

@@ -0,0 +1,204 @@
+import {
+  BaseFeatureDataAdapter,
+  BaseOptions,
+} from '@jbrowse/core/data_adapters/BaseAdapter'
+import { openLocation } from '@jbrowse/core/util/io'
+import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import { Region, Feature, SimpleFeature } from '@jbrowse/core/util'
+import IntervalTree from '@flatten-js/interval-tree'
+import { unzip } from '@gmod/bgzf-filehandle'
+
+function isGzip(buf: Buffer) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
+}
+
+export function featureData(
+  line: string,
+  uniqueId: string,
+  flip: boolean,
+  names?: string[],
+) {
+  const l = line.split('\t')
+  const ref1 = l[flip ? 3 : 0]
+  const start1 = +l[flip ? 4 : 1]
+  const end1 = +l[flip ? 5 : 2]
+  const ref2 = +l[!flip ? 3 : 0]
+  const start2 = +l[!flip ? 4 : 1]
+  const end2 = +l[!flip ? 5 : 2]
+  const name = l[6]
+  const score = +l[7]
+  const strand1 = parseStrand(l[8])
+  const strand2 = parseStrand(l[9])
+  const extra = l.slice(9)
+  const rest = names
+    ? Object.fromEntries(names.slice(9).map((n, idx) => [n, extra[idx]]))
+    : extra
+
+  return new SimpleFeature({
+    start: start1,
+    end: end1,
+    refName: ref1,
+    strand: strand1,
+    name,
+    ...rest,
+    score,
+    uniqueId,
+    mate: { refName: ref2, start: start2, end: end2, strand: strand2 },
+  })
+}
+
+function parseStrand(strand: string) {
+  if (strand === '+') {
+    return 1
+  } else if (strand === '-') {
+    return -1
+  } else if (strand === '.') {
+    return 0
+  } else {
+    return undefined
+  }
+}
+
+export default class BedpeAdapter extends BaseFeatureDataAdapter {
+  protected bedpeFeatures?: Promise<{
+    header: string
+    feats1: Record<string, string[]>
+    feats2: Record<string, string[]>
+    columnNames: string[]
+  }>
+
+  protected intervalTrees: {
+    [key: string]: Promise<IntervalTree | undefined> | undefined
+  } = {}
+
+  public static capabilities = ['getFeatures', 'getRefNames']
+
+  private async loadDataP(opts: BaseOptions = {}) {
+    const pm = this.pluginManager
+    const bedLoc = this.getConf('bedpeLocation')
+    const buf = await openLocation(bedLoc, pm).readFile(opts)
+    const buffer = isGzip(buf) ? await unzip(buf) : buf
+    // 512MB  max chrome string length is 512MB
+    if (buffer.length > 536_870_888) {
+      throw new Error('Data exceeds maximum string length (512MB)')
+    }
+    const data = new TextDecoder('utf8', { fatal: true }).decode(buffer)
+    const lines = data.split(/\n|\r\n|\r/).filter(f => !!f)
+    const headerLines = []
+    let i = 0
+    for (; i < lines.length && lines[i].startsWith('#'); i++) {
+      headerLines.push(lines[i])
+    }
+    const header = headerLines.join('\n')
+    const feats1 = {} as Record<string, string[]>
+    const feats2 = {} as Record<string, string[]>
+    for (; i < lines.length; i++) {
+      const line = lines[i]
+      const cols = line.split('\t')
+      const r1 = cols[0]
+      const r2 = cols[3]
+      if (!feats1[r1]) {
+        feats1[r1] = []
+      }
+      if (!feats2[r2]) {
+        feats2[r2] = []
+      }
+      feats1[r1].push(line)
+      feats2[r2].push(line)
+    }
+    const columnNames = this.getConf('columnNames')
+
+    return {
+      header,
+      feats1,
+      feats2,
+      columnNames,
+    }
+  }
+
+  private async loadData(opts: BaseOptions = {}) {
+    if (!this.bedpeFeatures) {
+      this.bedpeFeatures = this.loadDataP(opts).catch(e => {
+        this.bedpeFeatures = undefined
+        throw e
+      })
+    }
+
+    return this.bedpeFeatures
+  }
+
+  public async getRefNames(opts: BaseOptions = {}) {
+    const { feats1, feats2 } = await this.loadData(opts)
+    return [...new Set([...Object.keys(feats1), ...Object.keys(feats2)])]
+  }
+
+  async getHeader(opts: BaseOptions = {}) {
+    const { header } = await this.loadData(opts)
+    return header
+  }
+
+  async getNames() {
+    const { header, columnNames } = await this.loadData()
+    if (columnNames.length) {
+      return columnNames
+    }
+    const defs = header.split(/\n|\r\n|\r/).filter(f => !!f)
+    const defline = defs[defs.length - 1]
+    return defline?.includes('\t')
+      ? defline
+          .slice(1)
+          .split('\t')
+          .map(field => field.trim())
+      : undefined
+  }
+
+  private async loadFeatureTreeP(refName: string) {
+    const { feats1, feats2 } = await this.loadData()
+    const lines1 = feats1[refName]
+    const lines2 = feats2[refName]
+    const names = await this.getNames()
+
+    const intervalTree = new IntervalTree()
+    const ret1 = lines1?.map((f, i) => {
+      const uniqueId = `${this.id}-${refName}-${i}`
+      return featureData(f, uniqueId, false, names)
+    })
+    const ret2 = lines2?.map((f, i) => {
+      const uniqueId = `${this.id}-${refName}-${i}`
+      return featureData(f, uniqueId, true, names)
+    })
+
+    for (let i = 0; i < ret1.length; i++) {
+      const obj = ret1[i]
+      intervalTree.insert([obj.get('start'), obj.get('end')], obj)
+    }
+
+    for (let i = 0; i < ret2.length; i++) {
+      const obj = ret2[i]
+      intervalTree.insert([obj.get('start'), obj.get('end')], obj)
+    }
+
+    return intervalTree
+  }
+
+  private async loadFeatureTree(refName: string) {
+    if (!this.intervalTrees[refName]) {
+      this.intervalTrees[refName] = this.loadFeatureTreeP(refName).catch(e => {
+        this.intervalTrees[refName] = undefined
+        throw e
+      })
+    }
+    return this.intervalTrees[refName]
+  }
+
+  public getFeatures(query: Region, opts: BaseOptions = {}) {
+    return ObservableCreate<Feature>(async observer => {
+      const { start, end, refName } = query
+      const intervalTree = await this.loadFeatureTree(refName)
+      intervalTree?.search([start, end]).forEach(f => observer.next(f))
+      observer.complete()
+    }, opts.signal)
+  }
+
+  public freeResources(): void {}
+}

plugins/bed/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

plugins/bed/src/BedpeAdapter/index.ts

@@ -0,0 +1,15 @@
+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',
+        configSchema,
+        getAdapterClass: () => import('./BedpeAdapter').then(r => r.default),
+      }),
+  )
+}

plugins/bed/src/BigBedAdapter/index.ts

@@ -1 +1,15 @@
-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',
+        configSchema,
+        getAdapterClass: () => import('./BigBedAdapter').then(r => r.default),
+      }),
+  )
+}

plugins/bed/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) => {