@jbrowse/plugin-bed 2.6.1 → 2.6.3

package/src/BedAdapter/BedAdapter.ts

@@ -1,171 +0,0 @@
-import BED from '@gmod/bed'
-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 } from '@jbrowse/core/util'
-import { featureData } from '../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 default class BedAdapter extends BaseFeatureDataAdapter {
-  protected bedFeatures?: Promise<{
-    header: string
-    features: Record<string, string[]>
-    parser: BED
-    columnNames: string[]
-    scoreColumn: string
-    colRef: number
-    colStart: number
-    colEnd: number
-  }>
-
-  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('bedLocation')
-    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 features = {} as Record<string, string[]>
-    for (; i < lines.length; i++) {
-      const line = lines[i]
-      const tab = line.indexOf('\t')
-      const refName = line.slice(0, tab)
-      if (!features[refName]) {
-        features[refName] = []
-      }
-      features[refName].push(line)
-    }
-
-    const autoSql = this.getConf('autoSql') as string
-    const parser = new BED({ autoSql })
-    const columnNames = this.getConf('columnNames')
-    const scoreColumn = this.getConf('scoreColumn')
-    const colRef = this.getConf('colRef')
-    const colStart = this.getConf('colStart')
-    const colEnd = this.getConf('colEnd')
-
-    return {
-      header,
-      features,
-      parser,
-      columnNames,
-      scoreColumn,
-      colRef,
-      colStart,
-      colEnd,
-    }
-  }
-
-  private async loadData(opts: BaseOptions = {}) {
-    if (!this.bedFeatures) {
-      this.bedFeatures = this.loadDataP(opts).catch(e => {
-        this.bedFeatures = undefined
-        throw e
-      })
-    }
-
-    return this.bedFeatures
-  }
-
-  public async getRefNames(opts: BaseOptions = {}) {
-    const { features } = await this.loadData(opts)
-    return Object.keys(features)
-  }
-
-  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.at(-1)
-    return defline?.includes('\t')
-      ? defline
-          .slice(1)
-          .split('\t')
-          .map(field => field.trim())
-      : undefined
-  }
-
-  private async loadFeatureIntervalTreeHelper(refName: string) {
-    const { colRef, colStart, colEnd, features, parser, scoreColumn } =
-      await this.loadData()
-    const lines = features[refName]
-    if (!lines) {
-      return undefined
-    }
-    const names = await this.getNames()
-
-    const intervalTree = new IntervalTree()
-    const ret = lines.map((f, i) => {
-      const uniqueId = `${this.id}-${refName}-${i}`
-      return featureData(
-        f,
-        colRef,
-        colStart,
-        colEnd,
-        scoreColumn,
-        parser,
-        uniqueId,
-        names,
-      )
-    })
-
-    for (const obj of ret) {
-      intervalTree.insert([obj.get('start'), obj.get('end')], obj)
-    }
-    return intervalTree
-  }
-
-  private async loadFeatureIntervalTree(refName: string) {
-    if (!this.intervalTrees[refName]) {
-      this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(
-        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.loadFeatureIntervalTree(refName)
-      intervalTree?.search([start, end]).forEach(f => observer.next(f))
-      observer.complete()
-    }, opts.signal)
-  }
-
-  public freeResources(): void {}
-}

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

@@ -1,437 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adapter can fetch bed with header 1`] = `
-[
-  {
-    "end": 3009,
-    "refName": "contigA",
-    "start": 3000,
-    "strand": 0,
-    "uniqueId": "test-contigA-0",
-  },
-  {
-    "end": 3114,
-    "refName": "contigA",
-    "start": 3105,
-    "strand": 0,
-    "uniqueId": "test-contigA-1",
-  },
-  {
-    "end": 3161,
-    "refName": "contigA",
-    "start": 3152,
-    "strand": 0,
-    "uniqueId": "test-contigA-2",
-  },
-  {
-    "end": 3180,
-    "refName": "contigA",
-    "start": 3171,
-    "strand": 0,
-    "uniqueId": "test-contigA-3",
-  },
-  {
-    "end": 3183,
-    "refName": "contigA",
-    "start": 3174,
-    "strand": 0,
-    "uniqueId": "test-contigA-4",
-  },
-  {
-    "end": 3222,
-    "refName": "contigA",
-    "start": 3213,
-    "strand": 0,
-    "uniqueId": "test-contigA-5",
-  },
-  {
-    "end": 3474,
-    "refName": "contigA",
-    "start": 3465,
-    "strand": 0,
-    "uniqueId": "test-contigA-6",
-  },
-  {
-    "end": 3804,
-    "refName": "contigA",
-    "start": 3795,
-    "strand": 0,
-    "uniqueId": "test-contigA-7",
-  },
-  {
-    "end": 4044,
-    "refName": "contigA",
-    "start": 4035,
-    "strand": 0,
-    "uniqueId": "test-contigA-8",
-  },
-  {
-    "end": 4082,
-    "refName": "contigA",
-    "start": 4073,
-    "strand": 0,
-    "uniqueId": "test-contigA-9",
-  },
-]
-`;
-
-exports[`adapter can fetch features bed with autosql 1`] = `
-[
-  {
-    "Entrez_Gene_Id": "2782",
-    "Hugo_Symbol": "GNB1",
-    "Matched_Norm_Sample_Barcode": "TCGA-OR-A5KB-11A-11D-A30A-10",
-    "Reference_Allele": "T",
-    "Tumor_Sample_Barcode": "TCGA-OR-A5KB-01A-11D-A30A-10",
-    "Tumor_Seq_Allele1": "T",
-    "Tumor_Seq_Allele2": "G",
-    "Variant_Classification": "Splice_Region",
-    "Variant_Type": "SNP",
-    "alcohol_history": "--",
-    "alcohol_intensity": "--",
-    "bmi": "--",
-    "case_id": "09454ed6-64bc-4a35-af44-7c4344623d45",
-    "cigarettes_per_day": "--",
-    "days_to_death": "--",
-    "dbSNP_RS": "novel",
-    "dbSNP_Val_Status": "",
-    "end": 10,
-    "ethnicity": "not hispanic or latino",
-    "freq": "0.0108695652174",
-    "gender": "female",
-    "height": "--",
-    "name": "T>G",
-    "project_id": "TCGA-ACC",
-    "refName": "ctgA",
-    "reserved": "0,0,0",
-    "sampleCount": "1",
-    "score": 1,
-    "start": 1,
-    "strand": 0,
-    "subfeatures": [
-      {
-        "end": 2,
-        "parentId": "test-ctgA-0",
-        "start": 1,
-        "strand": 0,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-ctgA-0-0",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-ctgA-0",
-    "weight": "--",
-    "years_smoked": "--",
-  },
-]
-`;
-
-exports[`adapter can fetch features from volvox.sort.bed simple bed3 1`] = `
-[
-  {
-    "end": 3009,
-    "refName": "contigA",
-    "start": 3000,
-    "strand": 0,
-    "uniqueId": "test-contigA-0",
-  },
-  {
-    "end": 3114,
-    "refName": "contigA",
-    "start": 3105,
-    "strand": 0,
-    "uniqueId": "test-contigA-1",
-  },
-  {
-    "end": 3161,
-    "refName": "contigA",
-    "start": 3152,
-    "strand": 0,
-    "uniqueId": "test-contigA-2",
-  },
-  {
-    "end": 3180,
-    "refName": "contigA",
-    "start": 3171,
-    "strand": 0,
-    "uniqueId": "test-contigA-3",
-  },
-  {
-    "end": 3183,
-    "refName": "contigA",
-    "start": 3174,
-    "strand": 0,
-    "uniqueId": "test-contigA-4",
-  },
-  {
-    "end": 3222,
-    "refName": "contigA",
-    "start": 3213,
-    "strand": 0,
-    "uniqueId": "test-contigA-5",
-  },
-  {
-    "end": 3474,
-    "refName": "contigA",
-    "start": 3465,
-    "strand": 0,
-    "uniqueId": "test-contigA-6",
-  },
-  {
-    "end": 3804,
-    "refName": "contigA",
-    "start": 3795,
-    "strand": 0,
-    "uniqueId": "test-contigA-7",
-  },
-  {
-    "end": 4044,
-    "refName": "contigA",
-    "start": 4035,
-    "strand": 0,
-    "uniqueId": "test-contigA-8",
-  },
-  {
-    "end": 4082,
-    "refName": "contigA",
-    "start": 4073,
-    "strand": 0,
-    "uniqueId": "test-contigA-9",
-  },
-]
-`;
-
-exports[`adapter can fetch features from volvox-bed12.bed 1`] = `
-[
-  {
-    "end": 9000,
-    "itemRgb": "0,0,0",
-    "name": "EDEN.1",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 1049,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 1200,
-        "parentId": "test-ctgA-0",
-        "start": 1049,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-ctgA-0-0",
-      },
-      {
-        "end": 1500,
-        "parentId": "test-ctgA-0",
-        "start": 1200,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-0-1",
-      },
-      {
-        "end": 3902,
-        "parentId": "test-ctgA-0",
-        "start": 2999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-0-2",
-      },
-      {
-        "end": 5500,
-        "parentId": "test-ctgA-0",
-        "start": 4999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-0-3",
-      },
-      {
-        "end": 7608,
-        "parentId": "test-ctgA-0",
-        "start": 6999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-0-4",
-      },
-      {
-        "end": 9000,
-        "parentId": "test-ctgA-0",
-        "start": 7608,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-ctgA-0-5",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-ctgA-0",
-  },
-  {
-    "end": 9000,
-    "itemRgb": "0,0,0",
-    "name": "EDEN.2",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 1049,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 1200,
-        "parentId": "test-ctgA-1",
-        "start": 1049,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-ctgA-1-0",
-      },
-      {
-        "end": 1500,
-        "parentId": "test-ctgA-1",
-        "start": 1200,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-1-1",
-      },
-      {
-        "end": 5500,
-        "parentId": "test-ctgA-1",
-        "start": 4999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-1-2",
-      },
-      {
-        "end": 7608,
-        "parentId": "test-ctgA-1",
-        "start": 6999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-1-3",
-      },
-      {
-        "end": 9000,
-        "parentId": "test-ctgA-1",
-        "start": 7608,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-ctgA-1-4",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-ctgA-1",
-  },
-  {
-    "end": 9000,
-    "itemRgb": "0,0,0",
-    "name": "EDEN.3",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 1299,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 1500,
-        "parentId": "test-ctgA-2",
-        "start": 1299,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-ctgA-2-0",
-      },
-      {
-        "end": 3300,
-        "parentId": "test-ctgA-2",
-        "start": 2999,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-ctgA-2-1",
-      },
-      {
-        "end": 3902,
-        "parentId": "test-ctgA-2",
-        "start": 3300,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-2-2",
-      },
-      {
-        "end": 5500,
-        "parentId": "test-ctgA-2",
-        "start": 4999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-2-3",
-      },
-      {
-        "end": 7600,
-        "parentId": "test-ctgA-2",
-        "start": 6999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-2-4",
-      },
-      {
-        "end": 9000,
-        "parentId": "test-ctgA-2",
-        "start": 7600,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-ctgA-2-5",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-ctgA-2",
-  },
-  {
-    "end": 23000,
-    "itemRgb": "0,0,0",
-    "name": "rna-Apple3",
-    "refName": "ctgA",
-    "score": 1000,
-    "start": 17399,
-    "strand": 1,
-    "subfeatures": [
-      {
-        "end": 17999,
-        "parentId": "test-ctgA-3",
-        "start": 17399,
-        "strand": 1,
-        "type": "five_prime_UTR",
-        "uniqueId": "test-ctgA-3-0",
-      },
-      {
-        "end": 18800,
-        "parentId": "test-ctgA-3",
-        "start": 17999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-3-1",
-      },
-      {
-        "end": 19500,
-        "parentId": "test-ctgA-3",
-        "start": 18999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-3-2",
-      },
-      {
-        "end": 21200,
-        "parentId": "test-ctgA-3",
-        "start": 20999,
-        "strand": 1,
-        "type": "CDS",
-        "uniqueId": "test-ctgA-3-3",
-      },
-      {
-        "end": 23000,
-        "parentId": "test-ctgA-3",
-        "start": 21200,
-        "strand": 1,
-        "type": "three_prime_UTR",
-        "uniqueId": "test-ctgA-3-4",
-      },
-    ],
-    "type": "mRNA",
-    "uniqueId": "test-ctgA-3",
-  },
-]
-`;
-
-exports[`adapter can use gwas header 1`] = `[]`;

package/src/BedAdapter/configSchema.ts

@@ -1,69 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config BedAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const BedAdapter = ConfigurationSchema(
-  'BedAdapter',
-  {
-    /**
-     * #slot
-     */
-    bedLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },
-    },
-    /**
-     * #slot
-     */
-    columnNames: {
-      type: 'stringArray',
-      description: 'List of column names',
-      defaultValue: [],
-    },
-    /**
-     * #slot
-     */
-    scoreColumn: {
-      type: 'string',
-      description: 'The column to use as a "score" attribute',
-      defaultValue: '',
-    },
-    /**
-     * #slot
-     */
-    autoSql: {
-      type: 'string',
-      description: 'The autoSql definition for the data fields in the file',
-      defaultValue: '',
-    },
-    /**
-     * #slot
-     */
-    colRef: {
-      type: 'number',
-      description: 'The column to use as a "refName" attribute',
-      defaultValue: 0,
-    },
-    /**
-     * #slot
-     */
-    colStart: {
-      type: 'number',
-      description: 'The column to use as a "start" attribute',
-      defaultValue: 1,
-    },
-    /**
-     * #slot
-     */
-    colEnd: {
-      type: 'number',
-      description: 'The column to use as a "end" attribute',
-      defaultValue: 2,
-    },
-  },
-  { explicitlyTyped: true },
-)
-export default BedAdapter

package/src/BedAdapter/index.ts

@@ -1,16 +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: 'BedAdapter',
-        displayName: 'BED adapter',
-        configSchema,
-        getAdapterClass: () => import('./BedAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/BedAdapter/test_data/gwas.bed

@@ -1,20 +0,0 @@
-#chrom	pos	rsid	ref	alt	neg_log_pvalue	beta	stderr_beta	alt_allele_freq
-1	721290	rs12565286	G	C	0.275233	.	.	.
-1	752566	rs3094315	G	A	0.0315638	.	.	.
-1	775659	rs2905035	A	G	0.183626	.	.	.
-1	777122	rs2980319	A	T	0.207258	.	.	.
-1	779322	rs4040617	A	G	0.0326393	.	.	.
-1	780785	rs2977612	T	A	0.0225965	.	.	.
-1	785050	rs2905062	G	A	0.0346572	.	.	.
-1	785989	rs2980300	T	C	0.00638744	.	.	.
-1	798959	rs11240777	G	A	0.49853	.	.	.
-1	990380	.	C	A,G,T	0.136915	.	.	.
-1	998501	rs3813193	G	C	0.450384	.	.	.
-1	1003629	rs4075116	C	T	0.881074	.	.	.
-1	1005806	rs3934834	C	T	0.756218	.	.	.
-1	1017170	rs3766193	C	G	0.336111	.	.	.
-1	1017197	rs3766192	C	T	0.381743	.	.	.
-1	1017587	rs3766191	C	T	0.775467	.	.	.
-1	1018562	rs9442371	C	T	0.233364	.	.	.
-1	1018704	rs9442372	A	G	0.248721	.	.	.
-1	1021346	rs10907177	A	G	0.842846	.	.	.