@jbrowse/plugin-variants 2.6.1 → 2.6.2

package/src/VcfFeature/util.ts

@@ -1,138 +0,0 @@
-import VCF, { parseBreakend } from '@gmod/vcf'
-
-const altTypeToSO: { [key: string]: string | undefined } = {
-  DEL: 'deletion',
-  INS: 'insertion',
-  DUP: 'duplication',
-  INV: 'inversion',
-  INVDUP: 'inverted duplication',
-  CNV: 'copy_number_variation',
-  TRA: 'translocation',
-  'DUP:TANDEM': 'tandem_duplication',
-  NON_REF: 'sequence_variant',
-  '*': 'sequence_variant',
-}
-
-/**
- * Get a sequence ontology (SO) term that describes the variant type
- */
-export function getSOTermAndDescription(
-  ref: string,
-  alt: string[],
-  parser: VCF,
-): string[] {
-  // it's just a remark if there are no alternate alleles
-  if (!alt || alt.length === 0) {
-    return ['remark', 'no alternative alleles']
-  }
-
-  const soTerms = new Set<string>()
-  let descriptions = new Set<string>()
-  alt.forEach(a => {
-    let [soTerm, description] = getSOAndDescFromAltDefs(ref, a, parser)
-    if (!soTerm) {
-      ;[soTerm, description] = getSOAndDescByExamination(ref, a)
-    }
-    if (soTerm && description) {
-      soTerms.add(soTerm)
-      descriptions.add(description)
-    }
-  })
-
-  // Combine descriptions like ["SNV G -> A", "SNV G -> T"] to ["SNV G -> A,T"]
-  if (descriptions.size > 1) {
-    const descs = [...descriptions]
-    const prefixes = new Set(
-      descs.map(desc => {
-        const prefix = desc.split('->')
-        return prefix[1] ? prefix[0] : desc
-      }),
-    )
-
-    descriptions = new Set(
-      [...prefixes].map(prefix => {
-        const suffixes = descs
-          .map(desc => {
-            const pref = desc.split('-> ')
-            return pref[1] && pref[0] === prefix ? pref[1] : ''
-          })
-          .filter(f => !!f)
-
-        return suffixes.length ? prefix + '-> ' + suffixes.join(',') : prefix
-      }),
-    )
-  }
-  if (soTerms.size) {
-    return [[...soTerms].join(','), [...descriptions].join(',')]
-  }
-  return []
-}
-
-export function getSOAndDescFromAltDefs(
-  ref: string,
-  alt: string,
-  parser: VCF,
-): string[] {
-  if (typeof alt === 'string' && !alt.startsWith('<')) {
-    return []
-  }
-
-  // look for a definition with an SO type for this
-  let soTerm = altTypeToSO[alt]
-  // if no SO term but ALT is in metadata, assume sequence_variant
-  if (!soTerm && parser.getMetadata('ALT', alt)) {
-    soTerm = 'sequence_variant'
-  }
-  if (soTerm) {
-    return [soTerm, alt]
-  }
-
-  // try to look for a definition for a parent term if we can
-  const modAlt = alt.split(':')
-  if (modAlt.length > 1) {
-    return getSOAndDescFromAltDefs(
-      ref,
-      `<${modAlt.slice(0, -1).join(':')}>`,
-      parser,
-    )
-  }
-
-  // no parent
-  return []
-}
-
-// note: term SNV is used instead of SNP because SO definition of SNP says
-// abundance must be at least 1% in population, and can't be sure we meet
-// that
-export function getSOAndDescByExamination(ref: string, alt: string) {
-  const bnd = parseBreakend(alt)
-  if (bnd) {
-    return ['breakend', alt]
-  } else if (ref.length === 1 && alt.length === 1) {
-    return ['SNV', makeDescriptionString('SNV', ref, alt)]
-  } else if (alt === '<INS>') {
-    return ['insertion', alt]
-  } else if (alt === '<DEL>') {
-    return ['deletion', alt]
-  } else if (alt === '<INV>') {
-    return ['deletion', alt]
-  } else if (alt === '<TRA>') {
-    return ['translocation', alt]
-  } else if (alt.includes('<')) {
-    return ['sv', alt]
-  } else if (ref.length === alt.length) {
-    return ref.split('').reverse().join('') === alt
-      ? ['inversion', makeDescriptionString('inversion', ref, alt)]
-      : ['substitution', makeDescriptionString('substitution', ref, alt)]
-  } else if (ref.length <= alt.length) {
-    return ['insertion', makeDescriptionString('insertion', ref, alt)]
-  } else if (ref.length > alt.length) {
-    return ['deletion', makeDescriptionString('deletion', ref, alt)]
-  }
-
-  return ['indel', makeDescriptionString('indel', ref, alt)]
-}
-
-function makeDescriptionString(soTerm: string, ref: string, alt: string) {
-  return `${soTerm} ${ref} -> ${alt}`
-}

package/src/VcfTabixAdapter/VcfTabixAdapter.test.ts

@@ -1,69 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import Adapter from './VcfTabixAdapter'
-import configSchema from './configSchema'
-
-test('adapter can fetch variants from volvox.vcf.gz', async () => {
-  const adapter = new Adapter(
-    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',
-        },
-      },
-    }),
-  )
-
-  const csiAdapter = new Adapter(
-    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',
-        },
-      },
-    }),
-  )
-
-  const csiFeatures = csiAdapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-  })
-
-  const names = await adapter.getRefNames()
-  const csiNames = await csiAdapter.getRefNames()
-  expect(names).toEqual(csiNames)
-  expect(names).toMatchSnapshot()
-
-  const feat = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-  })
-
-  const featArray = await firstValueFrom(feat.pipe(toArray()))
-  const csiFeaturesArray = await firstValueFrom(csiFeatures.pipe(toArray()))
-  expect(featArray.slice(0, 5)).toMatchSnapshot()
-  expect(csiFeaturesArray.slice(0, 5)).toEqual(featArray.slice(0, 5))
-
-  const featNonExist = adapter.getFeatures({
-    refName: 'ctgC',
-    start: 0,
-    end: 20000,
-  })
-
-  const featArrayNonExist = await firstValueFrom(featNonExist.pipe(toArray()))
-  expect(featArrayNonExist).toEqual([])
-})

package/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -1,90 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { NoAssemblyRegion } 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'
-import { TabixIndexedFile } from '@gmod/tabix'
-import VcfParser from '@gmod/vcf'
-
-// local
-import VcfFeature from '../VcfFeature'
-
-export default class extends BaseFeatureDataAdapter {
-  private configured?: Promise<{
-    vcf: TabixIndexedFile
-    parser: VcfParser
-  }>
-
-  private async configurePre() {
-    const pm = this.pluginManager
-    const vcfGzLocation = this.getConf('vcfGzLocation')
-    const location = this.getConf(['index', 'location'])
-    const indexType = this.getConf(['index', 'indexType'])
-
-    const filehandle = openLocation(vcfGzLocation, pm)
-    const isCSI = indexType === 'CSI'
-    const vcf = new TabixIndexedFile({
-      filehandle,
-      csiFilehandle: isCSI ? openLocation(location, pm) : undefined,
-      tbiFilehandle: !isCSI ? openLocation(location, pm) : undefined,
-      chunkCacheSize: 50 * 2 ** 20,
-      chunkSizeLimit: 1000000000,
-    })
-
-    const header = await vcf.getHeader()
-    return {
-      vcf,
-      parser: new VcfParser({ header }),
-    }
-  }
-
-  protected async configure() {
-    if (!this.configured) {
-      this.configured = this.configurePre().catch(e => {
-        this.configured = undefined
-        throw e
-      })
-    }
-    return this.configured
-  }
-
-  public async getRefNames(opts: BaseOptions = {}) {
-    const { vcf } = await this.configure()
-    return vcf.getReferenceSequenceNames(opts)
-  }
-
-  async getHeader() {
-    const { vcf } = await this.configure()
-    return vcf.getHeader()
-  }
-
-  async getMetadata() {
-    const { parser } = await this.configure()
-    return parser.getMetadata()
-  }
-
-  public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      const { refName, start, end } = query
-      const { vcf, parser } = await this.configure()
-      await vcf.getLines(refName, start, end, {
-        lineCallback: (line, fileOffset) => {
-          observer.next(
-            new VcfFeature({
-              variant: parser.parseLine(line),
-              parser,
-              id: `${this.id}-vcf-${fileOffset}`,
-            }),
-          )
-        },
-        ...opts,
-      })
-      observer.complete()
-    }, opts.signal)
-  }
-
-  public freeResources(/* { region } */): void {}
-}

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

@@ -1,325 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch variants from volvox.vcf.gz 1`] = `
-[
-  "ctgA",
-]
-`;
-
-exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
-[
-  {
-    "ALT": [
-      "C",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        3,
-      ],
-      "DP4": [
-        0,
-        0,
-        3,
-        0,
-      ],
-      "FQ": [
-        -36,
-      ],
-      "MQ": [
-        37,
-      ],
-      "VDB": [
-        0.0186,
-      ],
-    },
-    "POS": 277,
-    "QUAL": 10.4,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> C",
-    "end": 277,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          13,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          42,
-          9,
-          0,
-        ],
-      },
-    },
-    "start": 276,
-    "type": "SNV",
-    "uniqueId": "test-vcf-604453",
-  },
-  {
-    "ALT": [
-      "C",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        23,
-      ],
-      "DP4": [
-        0,
-        1,
-        8,
-        14,
-      ],
-      "FQ": [
-        -73,
-      ],
-      "MQ": [
-        37,
-      ],
-      "PV4": [
-        1,
-        1,
-        0.42,
-        1,
-      ],
-      "VDB": [
-        0.0308,
-      ],
-    },
-    "POS": 1694,
-    "QUAL": 107,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> C",
-    "end": 1694,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          89,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          140,
-          46,
-          0,
-        ],
-      },
-    },
-    "start": 1693,
-    "type": "SNV",
-    "uniqueId": "test-vcf-604551",
-  },
-  {
-    "ALT": [
-      "G",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        1,
-      ],
-      "AF1": [
-        0.5,
-      ],
-      "DP": [
-        22,
-      ],
-      "DP4": [
-        6,
-        5,
-        3,
-        8,
-      ],
-      "FQ": [
-        45.3,
-      ],
-      "MQ": [
-        37,
-      ],
-      "PV4": [
-        0.39,
-        1,
-        1,
-        1,
-      ],
-      "VDB": [
-        0.0253,
-      ],
-    },
-    "POS": 2644,
-    "QUAL": 44,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> G",
-    "end": 2644,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          75,
-        ],
-        "GT": [
-          "0/1",
-        ],
-        "PL": [
-          74,
-          0,
-          77,
-        ],
-      },
-    },
-    "start": 2643,
-    "type": "SNV",
-    "uniqueId": "test-vcf-604668",
-  },
-  {
-    "ALT": [
-      "A",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        19,
-      ],
-      "DP4": [
-        0,
-        0,
-        8,
-        11,
-      ],
-      "FQ": [
-        -84,
-      ],
-      "MQ": [
-        36,
-      ],
-      "VDB": [
-        0.0384,
-      ],
-    },
-    "POS": 3213,
-    "QUAL": 124,
-    "REF": "T",
-    "aliases": undefined,
-    "description": "SNV T -> A",
-    "end": 3213,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          99,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          157,
-          57,
-          0,
-        ],
-      },
-    },
-    "start": 3212,
-    "type": "SNV",
-    "uniqueId": "test-vcf-604785",
-  },
-  {
-    "ALT": [
-      "ct",
-    ],
-    "CHROM": "ctgA",
-    "FILTER": null,
-    "ID": null,
-    "INFO": {
-      "AC1": [
-        2,
-      ],
-      "AF1": [
-        1,
-      ],
-      "DP": [
-        15,
-      ],
-      "DP4": [
-        0,
-        0,
-        5,
-        6,
-      ],
-      "FQ": [
-        -67.5,
-      ],
-      "INDEL": true,
-      "MQ": [
-        37,
-      ],
-      "VDB": [
-        0.0384,
-      ],
-    },
-    "POS": 3858,
-    "QUAL": 160,
-    "REF": "ctt",
-    "aliases": undefined,
-    "description": "deletion ctt -> ct",
-    "end": 3860,
-    "name": undefined,
-    "refName": "ctgA",
-    "samples": {
-      "sample_data/raw/volvox/volvox-sorted.bam": {
-        "GQ": [
-          63,
-        ],
-        "GT": [
-          "1/1",
-        ],
-        "PL": [
-          201,
-          33,
-          0,
-        ],
-      },
-    },
-    "start": 3857,
-    "type": "deletion",
-    "uniqueId": "test-vcf-604887",
-  },
-]
-`;

package/src/VcfTabixAdapter/configSchema.ts

@@ -1,43 +0,0 @@
-import { types } from 'mobx-state-tree'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config VcfTabixAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const VcfTabixAdapter = ConfigurationSchema(
-  'VcfTabixAdapter',
-  {
-    /**
-     * #slot
-     */
-    vcfGzLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },
-    },
-    index: ConfigurationSchema('VcfIndex', {
-      /**
-       * #slot index.indexType
-       */
-      indexType: {
-        model: types.enumeration('IndexType', ['TBI', 'CSI']),
-        type: 'stringEnum',
-        defaultValue: 'TBI',
-      },
-      /**
-       * #slot index.location
-       */
-      location: {
-        type: 'fileLocation',
-        defaultValue: {
-          uri: '/path/to/my.vcf.gz.tbi',
-          locationType: 'UriLocation',
-        },
-      },
-    }),
-  },
-  { explicitlyTyped: true },
-)
-
-export default VcfTabixAdapter

package/src/VcfTabixAdapter/index.ts

@@ -1,17 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import configSchema from './configSchema'
-
-export { default as configSchema } from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'VcfTabixAdapter',
-        displayName: 'VCF tabix adapter',
-        configSchema,
-        getAdapterClass: () => import('./VcfTabixAdapter').then(r => r.default),
-      }),
-  )
-}

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

@@ -1,20 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`plugin in a stock JBrowse 1`] = `{}`;
-
-exports[`plugin in a stock JBrowse 2`] = `
-{
-  "displays": [
-    {
-      "displayId": "trackId0-LinearVariantDisplay",
-      "type": "LinearVariantDisplay",
-    },
-    {
-      "displayId": "trackId0-ChordVariantDisplay",
-      "type": "ChordVariantDisplay",
-    },
-  ],
-  "trackId": "trackId0",
-  "type": "VariantTrack",
-}
-`;