@jbrowse/plugin-alignments 2.6.1 → 2.6.3

package/src/AlignmentsFeatureDetail/index.ts

@@ -1,33 +0,0 @@
-import { lazy } from 'react'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
-import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'
-import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget'
-
-const configSchema = ConfigurationSchema('AlignmentsFeatureWidget', {})
-
-export function stateModelFactory(pluginManager: PluginManager) {
-  const baseModel = baseModelFactory(pluginManager)
-  return types.compose(
-    baseModel,
-    types.model('AlignmentsFeatureWidget', {
-      type: types.literal('AlignmentsFeatureWidget'),
-    }),
-  )
-}
-
-export default function register(pluginManager: PluginManager) {
-  pluginManager.addWidgetType(
-    () =>
-      new WidgetType({
-        name: 'AlignmentsFeatureWidget',
-        heading: 'Feature details',
-        configSchema,
-        stateModel: stateModelFactory(pluginManager),
-        ReactComponent: lazy(() => import('./AlignmentsFeatureDetail')),
-      }),
-  )
-}
-
-export { configSchema }

package/src/AlignmentsFeatureDetail/util.ts

@@ -1,27 +0,0 @@
-import { getSession } from '@jbrowse/core/util'
-import { IAnyStateTreeNode } from 'mobx-state-tree'
-
-export function getTag(
-  tag: string,
-  feat: {
-    tags?: { [key: string]: unknown }
-    [key: string]: unknown
-  },
-) {
-  return feat.tags?.[tag] || feat[tag]
-}
-
-export async function navToLoc(locString: string, model: IAnyStateTreeNode) {
-  const session = getSession(model)
-  const { view } = model
-  try {
-    if (view) {
-      await view.navToLocString(locString)
-    } else {
-      throw new Error('No view associated with this view anymore')
-    }
-  } catch (e) {
-    console.error(e)
-    session.notify(`${e}`)
-  }
-}

package/src/AlignmentsTrack/configSchemaF.ts

@@ -1,22 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-/**
- * #config AlignmentsTrack
- * has very little config; most config and state logic is on the display
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-export default function configSchemaFactory(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'AlignmentsTrack',
-    {},
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: createBaseTrackConfig(pluginManager),
-    },
-  )
-}

package/src/AlignmentsTrack/index.ts

@@ -1,22 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
-import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
-import configSchemaF from './configSchemaF'
-
-export default function register(pm: PluginManager) {
-  pm.addTrackType(() => {
-    const configSchema = configSchemaF(pm)
-    const track = new TrackType({
-      name: 'AlignmentsTrack',
-      displayName: 'Alignments track',
-      configSchema,
-      stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema),
-    })
-    const linearAlignmentsDisplay = pm.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
-  })
-}

package/src/BamAdapter/BamAdapter.test.ts

@@ -1,124 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import Adapter from './BamAdapter'
-import configSchema from './configSchema'
-
-test('adapter can fetch features from volvox.bam', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      bamLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve('../../test_data/volvox-sorted.bam.bai'),
-          locationType: 'LocalPathLocation',
-        },
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-  })
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  expect(featuresArray[0].get('refName')).toBe('ctgA')
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.length).toEqual(3809)
-  expect(featuresJsonArray.slice(1000, 1010)).toMatchSnapshot()
-
-  expect(adapter.refIdToName(0)).toBe('ctgA')
-  expect(adapter.refIdToName(1)).toBe(undefined)
-
-  expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-
-  const adapterCSI = new Adapter(
-    configSchema.create({
-      bamLocation: {
-        localPath: require.resolve('../../test_data/volvox-sorted.bam'),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        indexType: 'CSI',
-        location: {
-          localPath: require.resolve('../../test_data/volvox-sorted.bam.csi'),
-          locationType: 'LocalPathLocation',
-        },
-      },
-    }),
-  )
-
-  const featuresCSI = adapterCSI.getFeatures({
-    assemblyName: 'volvox',
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-  })
-  const featuresArrayCSI = await firstValueFrom(featuresCSI.pipe(toArray()))
-  const featuresJsonArrayCSI = featuresArrayCSI.map(f => f.toJSON())
-  expect(featuresJsonArrayCSI).toEqual(featuresJsonArray)
-})
-
-test('test usage of BamSlightlyLazyFeature toJSON (used in the widget)', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      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 firstValueFrom(features.pipe(toArray()))
-  const f = featuresArray[0].toJSON()
-  expect(f.refName).toBe('ctgA')
-  expect(f.start).toBe(2)
-  expect(f.end).toBe(102)
-  expect(f.mismatches).not.toBeTruthy()
-})
-
-test('test usage of BamSlightlyLazyFeature for extended CIGAR', async () => {
-  const adapter = new Adapter(
-    configSchema.create({
-      bamLocation: {
-        localPath: require.resolve('../../test_data/extended_cigar.bam'),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve('../../test_data/extended_cigar.bam.bai'),
-          locationType: 'LocalPathLocation',
-        },
-        indexType: 'BAI',
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    assemblyName: 'hg19',
-    refName: '1',
-    start: 13260,
-    end: 13340,
-  })
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const f = featuresArray[0]
-  expect(f.get('mismatches')).toMatchSnapshot()
-})

package/src/BamAdapter/BamAdapter.ts

@@ -1,251 +0,0 @@
-import { BamFile } from '@gmod/bam'
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { Region } from '@jbrowse/core/util/types'
-import { bytesForRegions, updateStatus, Feature } from '@jbrowse/core/util'
-import { openLocation } from '@jbrowse/core/util/io'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-
-// locals
-import BamSlightlyLazyFeature from './BamSlightlyLazyFeature'
-
-interface Header {
-  idToName: string[]
-  nameToId: Record<string, number>
-}
-
-export default class BamAdapter extends BaseFeatureDataAdapter {
-  private samHeader?: Header
-
-  private setupP?: Promise<Header>
-  private configureP?: Promise<{
-    bam: BamFile
-    sequenceAdapter?: BaseFeatureDataAdapter
-  }>
-
-  // derived classes may not use the same configuration so a custom
-  // configure method allows derived classes to override this behavior
-  protected async configurePre() {
-    const bamLocation = this.getConf('bamLocation')
-    const location = this.getConf(['index', 'location'])
-    const indexType = this.getConf(['index', 'indexType'])
-    const pm = this.pluginManager
-    const csi = indexType === 'CSI'
-    const bam = new BamFile({
-      bamFilehandle: openLocation(bamLocation, pm),
-      csiFilehandle: csi ? openLocation(location, pm) : undefined,
-      baiFilehandle: !csi ? openLocation(location, pm) : undefined,
-
-      // chunkSizeLimit and fetchSizeLimit are more troublesome than
-      // helpful, and have given overly large values on the ultra long
-      // nanopore reads even with 500MB limits, so disabled with infinity
-      yieldThreadTime: Infinity,
-    })
-
-    const adapterConfig = this.getConf('sequenceAdapter')
-    if (adapterConfig && this.getSubAdapter) {
-      const { dataAdapter } = await this.getSubAdapter(adapterConfig)
-      return {
-        bam,
-        sequenceAdapter: dataAdapter as BaseFeatureDataAdapter,
-      }
-    } else {
-      return { bam }
-    }
-  }
-
-  protected async configure() {
-    if (!this.configureP) {
-      this.configureP = this.configurePre().catch(e => {
-        this.configureP = undefined
-        throw e
-      })
-    }
-    return this.configureP
-  }
-
-  async getHeader(opts?: BaseOptions) {
-    const { bam } = await this.configure()
-    return bam.getHeaderText(opts)
-  }
-
-  private async setupPre(opts?: BaseOptions) {
-    const { statusCallback = () => {} } = opts || {}
-    const { bam } = await this.configure()
-    this.samHeader = await updateStatus(
-      'Downloading index',
-      statusCallback,
-      async () => {
-        const samHeader = await bam.getHeader(opts)
-
-        // use the @SQ lines in the header to figure out the
-        // mapping between ref ref ID numbers and names
-        const idToName: string[] = []
-        const nameToId: Record<string, number> = {}
-        samHeader
-          ?.filter(l => l.tag === 'SQ')
-          .forEach((sqLine, refId) => {
-            sqLine.data.forEach(item => {
-              if (item.tag === 'SN') {
-                // this is the ref name
-                const refName = item.value
-                nameToId[refName] = refId
-                idToName[refId] = refName
-              }
-            })
-          })
-
-        return { idToName, nameToId }
-      },
-    )
-    return this.samHeader
-  }
-
-  async setup(opts?: BaseOptions) {
-    if (!this.setupP) {
-      this.setupP = this.setupPre(opts).catch(e => {
-        this.setupP = undefined
-        throw e
-      })
-    }
-    return this.setupP
-  }
-
-  async getRefNames(opts?: BaseOptions) {
-    const { idToName } = await this.setup(opts)
-    return idToName
-  }
-
-  private async seqFetch(refName: string, start: number, end: number) {
-    const { sequenceAdapter } = await this.configure()
-    const refSeqStore = sequenceAdapter
-    if (!refSeqStore) {
-      return undefined
-    }
-    if (!refName) {
-      return undefined
-    }
-
-    const features = refSeqStore.getFeatures({
-      refName,
-      start,
-      end,
-      assemblyName: '',
-    })
-
-    const seqChunks = await firstValueFrom(features.pipe(toArray()))
-
-    let sequence = ''
-    seqChunks
-      .sort((a, b) => a.get('start') - b.get('start'))
-      .forEach(chunk => {
-        const chunkStart = chunk.get('start')
-        const chunkEnd = chunk.get('end')
-        const trimStart = Math.max(start - chunkStart, 0)
-        const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart)
-        const trimLength = trimEnd - trimStart
-        const chunkSeq = chunk.get('seq') || chunk.get('residues')
-        sequence += chunkSeq.slice(trimStart, trimStart + trimLength)
-      })
-
-    if (sequence.length !== end - start) {
-      throw new Error(
-        `sequence fetch failed: fetching ${refName}:${(
-          start - 1
-        ).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(
-          end - start
-        ).toLocaleString()}`,
-      )
-    }
-    return sequence
-  }
-
-  getFeatures(
-    region: Region & { originalRefName?: string },
-    opts?: BaseOptions & {
-      filterBy: {
-        flagInclude: number
-        flagExclude: number
-        tagFilter: { tag: string; value: unknown }
-        readName: string
-      }
-    },
-  ) {
-    const { refName, start, end, originalRefName } = region
-    const { signal, filterBy, statusCallback = () => {} } = opts || {}
-    return ObservableCreate<Feature>(async observer => {
-      const { bam } = await this.configure()
-      await this.setup(opts)
-      const records = await updateStatus(
-        'Downloading alignments',
-        statusCallback,
-        () => bam.getRecordsForRange(refName, start, end, opts),
-      )
-
-      await updateStatus('Processing alignments', statusCallback, async () => {
-        const {
-          flagInclude = 0,
-          flagExclude = 0,
-          tagFilter,
-          readName,
-        } = filterBy || {}
-
-        for (const record of records) {
-          let ref: string | undefined
-          if (!record.get('MD')) {
-            ref = await this.seqFetch(
-              originalRefName || refName,
-              record.get('start'),
-              record.get('end'),
-            )
-          }
-
-          const flags = record.flags
-          if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
-            continue
-          }
-
-          if (tagFilter) {
-            const v = record.get(tagFilter.tag)
-            if (!(v === '*' ? v !== undefined : `${v}` === tagFilter.value)) {
-              continue
-            }
-          }
-
-          if (readName && record.get('name') !== readName) {
-            continue
-          }
-
-          observer.next(new BamSlightlyLazyFeature(record, this, ref))
-        }
-        observer.complete()
-      })
-    }, signal)
-  }
-
-  async getMultiRegionFeatureDensityStats(
-    regions: Region[],
-    opts?: BaseOptions,
-  ) {
-    const { bam } = await this.configure()
-    // this is a method to avoid calling on htsget adapters
-    if (bam.index) {
-      const bytes = await bytesForRegions(regions, bam)
-      const fetchSizeLimit = this.getConf('fetchSizeLimit')
-      return { bytes, fetchSizeLimit }
-    } else {
-      return super.getMultiRegionFeatureDensityStats(regions, opts)
-    }
-  }
-
-  freeResources(/* { region } */): void {}
-
-  // depends on setup being called before the BAM constructor
-  refIdToName(refId: number) {
-    return this.samHeader?.idToName[refId]
-  }
-}

package/src/BamAdapter/BamSlightlyLazyFeature.ts

@@ -1,149 +0,0 @@
-/* eslint-disable no-underscore-dangle */
-import {
-  Feature,
-  SimpleFeatureSerialized,
-} from '@jbrowse/core/util/simpleFeature'
-import { BamRecord } from '@gmod/bam'
-
-// locals
-import { getClip, getMismatches } from '../MismatchParser'
-import BamAdapter from './BamAdapter'
-
-export default class BamSlightlyLazyFeature implements Feature {
-  // uses parameter properties to automatically create fields on the class
-  // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
-  constructor(
-    private record: BamRecord,
-    private adapter: BamAdapter,
-    private ref?: string,
-  ) {}
-
-  _get_name() {
-    return this.record.get('name')
-  }
-
-  _get_type(): string {
-    return 'match'
-  }
-
-  _get_score(): number {
-    return this.record.get('mq')
-  }
-
-  _get_flags(): string {
-    return this.record.flags
-  }
-
-  _get_strand(): number {
-    return this.record.isReverseComplemented() ? -1 : 1
-  }
-
-  _get_pair_orientation() {
-    return this.record.isPaired() ? this.record.getPairOrientation() : undefined
-  }
-
-  _get_next_ref() {
-    return this.record.isPaired()
-      ? this.adapter.refIdToName(this.record._next_refid())
-      : undefined
-  }
-
-  _get_next_pos() {
-    return this.record.isPaired() ? this.record._next_pos() : undefined
-  }
-
-  _get_next_segment_position() {
-    return this.record.isPaired()
-      ? `${this.adapter.refIdToName(this.record._next_refid())}:${
-          this.record._next_pos() + 1
-        }`
-      : undefined
-  }
-
-  _get_seq() {
-    return this.record.getReadBases()
-  }
-
-  qualRaw() {
-    return this.record.qualRaw()
-  }
-
-  set() {}
-
-  tags() {
-    const properties = Object.getOwnPropertyNames(
-      BamSlightlyLazyFeature.prototype,
-    )
-
-    return [
-      ...new Set(
-        properties
-          .filter(
-            prop =>
-              prop.startsWith('_get_') &&
-              prop !== '_get_mismatches' &&
-              prop !== '_get_tags',
-          )
-          .map(methodName => methodName.replace('_get_', ''))
-          .concat(this.record._tags()),
-      ),
-    ]
-  }
-
-  id() {
-    return `${this.adapter.id}-${this.record.id()}`
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  get(field: string): any {
-    const methodName = `_get_${field}`
-    // @ts-expect-error
-    if (this[methodName]) {
-      // @ts-expect-error
-      return this[methodName]()
-    }
-    return this.record.get(field)
-  }
-
-  _get_refName() {
-    return this.adapter.refIdToName(this.record.seq_id())
-  }
-
-  parent() {
-    return undefined
-  }
-
-  children() {
-    return undefined
-  }
-
-  pairedFeature() {
-    return false
-  }
-
-  toJSON(): SimpleFeatureSerialized {
-    return {
-      ...Object.fromEntries(
-        this.tags()
-          .map(t => [t, this.get(t)])
-          .filter(elt => elt[1] !== undefined),
-      ),
-      uniqueId: this.id(),
-    }
-  }
-
-  _get_mismatches() {
-    return getMismatches(
-      this.get('CIGAR'),
-      this.get('MD'),
-      this.get('seq'),
-      this.ref,
-      this.qualRaw(),
-    )
-  }
-
-  _get_clipPos() {
-    const cigar = this.get('CIGAR') || ''
-    return getClip(cigar, this.get('strand'))
-  }
-}