@jbrowse/plugin-comparative-adapters 2.6.1 → 2.6.3

package/src/PAFAdapter/PAFAdapter.ts

@@ -1,181 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { Region } from '@jbrowse/core/util/types'
-import { doesIntersect2 } from '@jbrowse/core/util/range'
-import { openLocation } from '@jbrowse/core/util/io'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { Feature } from '@jbrowse/core/util'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { unzip } from '@gmod/bgzf-filehandle'
-import { MismatchParser } from '@jbrowse/plugin-alignments'
-
-// locals
-import SyntenyFeature from './SyntenyFeature'
-import { isGzip, parseLineByLine } from '../util'
-import {
-  getWeightedMeans,
-  flipCigar,
-  swapIndelCigar,
-  parsePAFLine,
-  PAFRecord,
-} from './util'
-
-const { parseCigar } = MismatchParser
-
-interface PAFOptions extends BaseOptions {
-  config?: AnyConfigurationModel
-}
-
-export default class PAFAdapter extends BaseFeatureDataAdapter {
-  private setupP?: Promise<PAFRecord[]>
-
-  public static capabilities = ['getFeatures', 'getRefNames']
-
-  async setup(opts?: BaseOptions) {
-    if (!this.setupP) {
-      this.setupP = this.setupPre(opts).catch(e => {
-        this.setupP = undefined
-        throw e
-      })
-    }
-    return this.setupP
-  }
-
-  async setupPre(opts?: BaseOptions) {
-    const pm = this.pluginManager
-    const pafLocation = openLocation(this.getConf('pafLocation'), pm)
-    const buffer = (await pafLocation.readFile(opts)) as Buffer
-    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
-    return parseLineByLine(buf, parsePAFLine)
-  }
-
-  async hasDataForRefName() {
-    // determining this properly is basically a call to getFeatures
-    // so is not really that important, and has to be true or else
-    // getFeatures is never called (BaseAdapter filters it out)
-    return true
-  }
-
-  getAssemblyNames() {
-    const assemblyNames = this.getConf('assemblyNames') as string[]
-    if (assemblyNames.length === 0) {
-      const query = this.getConf('queryAssembly') as string
-      const target = this.getConf('targetAssembly') as string
-      return [query, target]
-    }
-    return assemblyNames
-  }
-
-  async getRefNames(opts: BaseOptions = {}) {
-    // @ts-expect-error
-    const r1 = opts.regions?.[0].assemblyName
-    const feats = await this.setup(opts)
-
-    const idx = this.getAssemblyNames().indexOf(r1)
-    if (idx !== -1) {
-      const set = new Set<string>()
-      for (const feat of feats) {
-        set.add(idx === 0 ? feat.qname : feat.tname)
-      }
-      return [...set]
-    }
-    console.warn('Unable to do ref renaming on adapter')
-    return []
-  }
-
-  getFeatures(query: Region, opts: PAFOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      let pafRecords = await this.setup(opts)
-      const { config } = opts
-
-      // note: this is not the adapter config, it is responding to a display
-      // setting passed in via the opts parameter
-      if (config && readConfObject(config, 'colorBy') === 'meanQueryIdentity') {
-        pafRecords = getWeightedMeans(pafRecords)
-      }
-      const assemblyNames = this.getAssemblyNames()
-
-      // The index of the assembly name in the query list corresponds to the
-      // adapter in the subadapters list
-      const index = assemblyNames.indexOf(query.assemblyName)
-      const { start: qstart, end: qend, refName: qref, assemblyName } = query
-      if (index === -1) {
-        console.warn(`${assemblyName} not found in this adapter`)
-        observer.complete()
-      }
-
-      for (let i = 0; i < pafRecords.length; i++) {
-        const r = pafRecords[i]
-        let start = 0
-        let end = 0
-        let refName = ''
-        let mateName = ''
-        let mateStart = 0
-        let mateEnd = 0
-        const flip = index === 0
-        const assemblyName = assemblyNames[+!flip]
-        if (index === 0) {
-          start = r.qstart
-          end = r.qend
-          refName = r.qname
-          mateName = r.tname
-          mateStart = r.tstart
-          mateEnd = r.tend
-        } else {
-          start = r.tstart
-          end = r.tend
-          refName = r.tname
-          mateName = r.qname
-          mateStart = r.qstart
-          mateEnd = r.qend
-        }
-        const { extra, strand } = r
-        if (refName === qref && doesIntersect2(qstart, qend, start, end)) {
-          const { numMatches = 0, blockLen = 1, cg, ...rest } = extra
-
-          let CIGAR = extra.cg
-          if (extra.cg) {
-            if (flip && strand === -1) {
-              CIGAR = flipCigar(parseCigar(extra.cg)).join('')
-            } else if (flip) {
-              CIGAR = swapIndelCigar(extra.cg)
-            }
-          }
-
-          observer.next(
-            new SyntenyFeature({
-              uniqueId: i + assemblyName,
-              assemblyName,
-              start,
-              end,
-              type: 'match',
-              refName,
-              strand,
-              ...rest,
-              CIGAR,
-              syntenyId: i,
-              identity: numMatches / blockLen,
-              numMatches,
-              blockLen,
-              mate: {
-                start: mateStart,
-                end: mateEnd,
-                refName: mateName,
-                assemblyName: assemblyNames[+flip],
-              },
-            }),
-          )
-        }
-      }
-
-      observer.complete()
-    })
-  }
-
-  freeResources(/* { query } */): void {}
-}

package/src/PAFAdapter/SyntenyFeature.ts

@@ -1,15 +0,0 @@
-import { SimpleFeature } from '@jbrowse/core/util'
-import { MismatchParser } from '@jbrowse/plugin-alignments'
-
-// locals
-const { getMismatches } = MismatchParser
-
-export default class SyntenyFeature extends SimpleFeature {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  get(arg: string): any {
-    if (arg === 'mismatches') {
-      return getMismatches(this.get('CIGAR'))
-    }
-    return super.get(arg)
-  }
-}

package/src/PAFAdapter/configSchema.ts

@@ -1,50 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config PAFAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const PAFAdapter = ConfigurationSchema(
-  'PAFAdapter',
-  {
-    /**
-     * #slot
-     */
-    assemblyNames: {
-      type: 'stringArray',
-      defaultValue: [],
-      description:
-        'Array of assembly names to use for this file. The target assembly name is the first value in the array, query assembly name is the second',
-    },
-    /**
-     * #slot
-     */
-    targetAssembly: {
-      type: 'string',
-      defaultValue: '',
-      description: 'Alternative to assemblyNames: the target assembly name',
-    },
-    /**
-     * #slot
-     */
-    queryAssembly: {
-      type: 'string',
-      defaultValue: '',
-      description: 'Alternative to assemblyNames: the query assembly name',
-    },
-    /**
-     * #slot
-     */
-    pafLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: '/path/to/file.paf',
-        locationType: 'UriLocation',
-      },
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default PAFAdapter

package/src/PAFAdapter/index.ts

@@ -1,18 +0,0 @@
-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: 'PAFAdapter',
-        displayName: 'PAF adapter',
-        configSchema,
-        adapterMetadata: {
-          hiddenFromGUI: true,
-        },
-        getAdapterClass: () => import('./PAFAdapter').then(r => r.default),
-      }),
-  )
-}