@jbrowse/plugin-bed 2.6.1 → 2.6.3

package/src/BedAdapter/test_data/volvox-autosql.bed

@@ -1 +0,0 @@
-ctgA	1	10	T>G	1	.	1815756	1815757	0,0,0	1	1	0	1	0.0108695652174	GNB1	2782	Splice_Region	SNP	T	T	G	novel		--	--	--	--	--	--	--	--	female	TCGA-ACC	not hispanic or latino	TCGA-OR-A5KB-01A-11D-A30A-10	TCGA-OR-A5KB-11A-11D-A30A-10	09454ed6-64bc-4a35-af44-7c4344623d45

package/src/BedAdapter/test_data/volvox-bed12.bed

@@ -1,4 +0,0 @@
-ctgA	1049	9000	EDEN.1	1000	+	1200	7608	0,0,0	4	451,903,501,2001	0,1950,3950,5950	EDEN	EDEN	-	-	-
-ctgA	1049	9000	EDEN.2	1000	+	1200	7608	0,0,0	3	451,501,2001	0,3950,5950	EDEN	EDEN	-	-	-
-ctgA	1299	9000	EDEN.3	1000	+	3300	7600	0,0,0	4	201,903,501,2001	0,1700,3700,5700	EDEN	EDEN	-	-	-
-ctgA	17399	23000	rna-Apple3	1000	+	17999	21200	0,0,0	3	1401,501,2001	0,1600,3600	rna-Apple3	rna-Apple3	-	-	-

package/src/BedAdapter/test_data/volvox.sort.bed

@@ -1,109 +0,0 @@
-contigA	3000	3009
-contigA	3105	3114
-contigA	3152	3161
-contigA	3171	3180
-contigA	3174	3183
-contigA	3213	3222
-contigA	3465	3474
-contigA	3795	3804
-contigA	4035	4044
-contigA	4073	4082
-contigA	4074	4083
-contigA	4166	4175
-contigA	4179	4188
-contigA	4204	4213
-contigA	4248	4257
-contigA	4260	4269
-contigA	4577	4586
-contigA	4828	4837
-contigA	4901	4910
-contigA	5006	5015
-contigA	5051	5060
-contigA	5201	5210
-contigA	5260	5269
-contigA	5281	5290
-contigA	5349	5358
-contigA	5353	5362
-contigA	5423	5432
-contigA	5457	5466
-contigA	5548	5557
-contigA	5626	5635
-contigA	5835	5844
-contigA	5909	5918
-contigA	5927	5936
-contigA	5969	5978
-contigA	6070	6079
-contigA	6185	6194
-contigA	6285	6294
-contigA	6363	6372
-contigA	6559	6568
-contigA	6834	6843
-contigA	6908	6917
-contigA	6918	6927
-contigA	7141	7150
-contigA	7173	7182
-contigA	7569	7578
-contigA	7619	7628
-contigA	7654	7663
-contigA	7671	7680
-contigA	7707	7716
-contigA	7739	7748
-contigA	8077	8086
-contigA	8128	8137
-contigA	8132	8141
-contigA	8210	8219
-contigA	8267	8276
-contigA	8328	8337
-contigA	8524	8533
-contigA	8659	8668
-contigA	8660	8669
-contigA	8742	8751
-contigA	8811	8820
-contigA	8816	8825
-contigA	8964	8973
-contigA	9048	9057
-contigA	9054	9063
-contigA	9136	9145
-contigA	9243	9252
-contigA	9320	9329
-contigA	9366	9375
-contigA	9525	9534
-contigA	9580	9589
-contigA	9610	9619
-contigA	9744	9753
-contigA	9753	9762
-contigA	9759	9768
-contigA	9807	9816
-contigA	9853	9862
-contigA	9884	9893
-contigA	9920	9929
-contigA	10043	10052
-contigA	10216	10225
-contigA	10217	10226
-contigA	10252	10261
-contigA	10384	10393
-contigA	10498	10507
-contigA	10585	10594
-contigA	10684	10693
-contigA	10781	10790
-contigA	10875	10884
-contigA	11004	11013
-contigA	11095	11104
-contigA	11182	11191
-contigA	11207	11216
-contigA	11241	11250
-contigA	11335	11344
-contigA	11340	11349
-contigA	11535	11544
-contigA	11543	11552
-contigA	11549	11558
-contigA	11653	11662
-contigA	11675	11684
-contigA	11689	11698
-contigA	11774	11783
-contigA	11832	11841
-contigA	12386	12395
-contigA	12408	12417
-contigA	12441	12450
-contigA	12530	12539
-contigA	12738	12747

package/src/BedAdapter/test_data/volvox.sort.with.header.bed

@@ -1,121 +0,0 @@
-#this is a test header
-#this is a test header
-#this is a test header
-#this is a test header
-#this is a test header
-#this is a test header
-#this is a test header
-#this is a test header
-#this is a test header
-#this is a test header
-#this is a test header
-#this is a test header
-contigA	3000	3009
-contigA	3105	3114
-contigA	3152	3161
-contigA	3171	3180
-contigA	3174	3183
-contigA	3213	3222
-contigA	3465	3474
-contigA	3795	3804
-contigA	4035	4044
-contigA	4073	4082
-contigA	4074	4083
-contigA	4166	4175
-contigA	4179	4188
-contigA	4204	4213
-contigA	4248	4257
-contigA	4260	4269
-contigA	4577	4586
-contigA	4828	4837
-contigA	4901	4910
-contigA	5006	5015
-contigA	5051	5060
-contigA	5201	5210
-contigA	5260	5269
-contigA	5281	5290
-contigA	5349	5358
-contigA	5353	5362
-contigA	5423	5432
-contigA	5457	5466
-contigA	5548	5557
-contigA	5626	5635
-contigA	5835	5844
-contigA	5909	5918
-contigA	5927	5936
-contigA	5969	5978
-contigA	6070	6079
-contigA	6185	6194
-contigA	6285	6294
-contigA	6363	6372
-contigA	6559	6568
-contigA	6834	6843
-contigA	6908	6917
-contigA	6918	6927
-contigA	7141	7150
-contigA	7173	7182
-contigA	7569	7578
-contigA	7619	7628
-contigA	7654	7663
-contigA	7671	7680
-contigA	7707	7716
-contigA	7739	7748
-contigA	8077	8086
-contigA	8128	8137
-contigA	8132	8141
-contigA	8210	8219
-contigA	8267	8276
-contigA	8328	8337
-contigA	8524	8533
-contigA	8659	8668
-contigA	8660	8669
-contigA	8742	8751
-contigA	8811	8820
-contigA	8816	8825
-contigA	8964	8973
-contigA	9048	9057
-contigA	9054	9063
-contigA	9136	9145
-contigA	9243	9252
-contigA	9320	9329
-contigA	9366	9375
-contigA	9525	9534
-contigA	9580	9589
-contigA	9610	9619
-contigA	9744	9753
-contigA	9753	9762
-contigA	9759	9768
-contigA	9807	9816
-contigA	9853	9862
-contigA	9884	9893
-contigA	9920	9929
-contigA	10043	10052
-contigA	10216	10225
-contigA	10217	10226
-contigA	10252	10261
-contigA	10384	10393
-contigA	10498	10507
-contigA	10585	10594
-contigA	10684	10693
-contigA	10781	10790
-contigA	10875	10884
-contigA	11004	11013
-contigA	11095	11104
-contigA	11182	11191
-contigA	11207	11216
-contigA	11241	11250
-contigA	11335	11344
-contigA	11340	11349
-contigA	11535	11544
-contigA	11543	11552
-contigA	11549	11558
-contigA	11653	11662
-contigA	11675	11684
-contigA	11689	11698
-contigA	11774	11783
-contigA	11832	11841
-contigA	12386	12395
-contigA	12408	12417
-contigA	12441	12450
-contigA	12530	12539
-contigA	12738	12747

package/src/BedTabixAdapter/BedTabixAdapter.test.ts

@@ -1,196 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-import BedTabixAdapter from './BedTabixAdapter'
-import MyConfigSchema from './configSchema'
-
-test('adapter can fetch features from volvox-bed12.bed.gz', async () => {
-  const adapter = new BedTabixAdapter(
-    MyConfigSchema.create({
-      bedGzLocation: {
-        localPath: require.resolve('./test_data/volvox-bed12.bed.gz'),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve('./test_data/volvox-bed12.bed.gz.tbi'),
-          locationType: 'LocalPathLocation',
-        },
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-    assemblyName: 'volvox',
-  })
-  expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-  expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
-})
-
-test('adapter can fetch features from volvox.sort.bed.gz simple bed3', async () => {
-  const adapter = new BedTabixAdapter(
-    MyConfigSchema.create({
-      bedGzLocation: {
-        localPath: require.resolve('./test_data/volvox.sort.bed.gz'),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve('./test_data/volvox.sort.bed.gz.tbi'),
-          locationType: 'LocalPathLocation',
-        },
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    refName: 'contigA',
-    start: 0,
-    end: 20000,
-    assemblyName: 'volvox',
-  })
-  expect(await adapter.hasDataForRefName('contigA')).toBe(true)
-  expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
-})
-
-test('adapter can fetch features bed with autosql', async () => {
-  const adapter = new BedTabixAdapter(
-    MyConfigSchema.create({
-      bedGzLocation: {
-        localPath: require.resolve('./test_data/volvox-autosql.bed.gz'),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve('./test_data/volvox-autosql.bed.gz.tbi'),
-          locationType: 'LocalPathLocation',
-        },
-      },
-      autoSql: `table gdcCancer
-"somatic variants converted from MAF files obtained through the NCI GDC"
-    (
-    string chrom;      "Chromosome (or contig, scaffold, etc.)"
-    uint   chromStart; "Start position in chromosome"
-    uint   chromEnd;   "End position in chromosome"
-    string name;       "Name of item"
-    uint   score;      "Score from 0-1000"
-    char[1] strand;    "+ or -"
-    uint thickStart;   "Start of where display should be thick (start codon)"
-    uint thickEnd;     "End of where display should be thick (stop codon)"
-    uint reserved;     "Used as itemRgb as of 2004-11-22"
-    int blockCount;    "Number of blocks"
-    int[blockCount] blockSizes; "Comma separated list of block sizes"
-    int[blockCount] chromStarts; "Start positions relative to chromStart"
-    string sampleCount;    "Number of samples with this variant"
-    string freq;                    "Variant frequency"
-    lstring Hugo_Symbol;            "Hugo symbol"
-    lstring Entrez_Gene_Id;         "Entrez Gene Id"
-    lstring Variant_Classification; "Class of variant"
-    lstring Variant_Type;           "Type of variant"
-    lstring Reference_Allele;       "Reference allele"
-    lstring Tumor_Seq_Allele1;      "Tumor allele 1"
-    lstring Tumor_Seq_Allele2;      "Tumor allele 2"
-    lstring dbSNP_RS;               "dbSNP RS number"
-    lstring dbSNP_Val_Status;       "dbSNP validation status"
-    lstring days_to_death;          "Number of days till death"
-    lstring cigarettes_per_day;     "Number of cigarettes per day"
-    lstring weight;                 "Weight"
-    lstring alcohol_history;        "Any alcohol consumption?"
-    lstring alcohol_intensity;      "Frequency of alcohol consumption"
-    lstring bmi;                    "Body mass index"
-    lstring years_smoked;           "Number of years smoked"
-    lstring height;                 "Height"
-    lstring gender;                 "Gender"
-    lstring project_id;             "TCGA Project id"
-    lstring ethnicity;              "Ethnicity"
-    lstring Tumor_Sample_Barcode;   "Tumor sample barcode"
-    lstring Matched_Norm_Sample_Barcode;  "Matcheds normal sample barcode"
-    lstring case_id;                "Case ID number"
-)`,
-    }),
-  )
-  const features = adapter.getFeatures({
-    refName: 'ctgA',
-    start: 0,
-    end: 20000,
-    assemblyName: 'volvox',
-  })
-  expect(await adapter.hasDataForRefName('ctgA')).toBe(true)
-  expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
-})
-
-test('adapter can fetch bed with header', async () => {
-  const adapter = new BedTabixAdapter(
-    MyConfigSchema.create({
-      bedGzLocation: {
-        localPath: require.resolve(
-          './test_data/volvox.sort.with.header.bed.gz',
-        ),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve(
-            './test_data/volvox.sort.with.header.bed.gz.tbi',
-          ),
-          locationType: 'LocalPathLocation',
-        },
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    refName: 'contigA',
-    start: 0,
-    end: 20000,
-    assemblyName: 'volvox',
-  })
-  expect(await adapter.hasDataForRefName('contigA')).toBe(true)
-  expect(await adapter.hasDataForRefName('ctgB')).toBe(false)
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
-})
-
-test('adapter can use gwas header', async () => {
-  const adapter = new BedTabixAdapter(
-    MyConfigSchema.create({
-      bedGzLocation: {
-        localPath: require.resolve('./test_data/gwas.bed.gz'),
-        locationType: 'LocalPathLocation',
-      },
-      index: {
-        location: {
-          localPath: require.resolve('./test_data/gwas.bed.gz.tbi'),
-          locationType: 'LocalPathLocation',
-        },
-      },
-    }),
-  )
-
-  const features = adapter.getFeatures({
-    refName: '1',
-    start: 0,
-    end: 100_000,
-    assemblyName: 'hg19',
-  })
-
-  const featuresArray = await firstValueFrom(features.pipe(toArray()))
-  const featuresJsonArray = featuresArray.map(f => f.toJSON())
-  expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot()
-})

package/src/BedTabixAdapter/BedTabixAdapter.ts

@@ -1,105 +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 { FileLocation, Region, Feature } from '@jbrowse/core/util'
-import { TabixIndexedFile } from '@gmod/tabix'
-import { featureData } from '../util'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-
-export default class BedTabixAdapter extends BaseFeatureDataAdapter {
-  private parser: BED
-
-  protected bed: TabixIndexedFile
-
-  protected columnNames: string[]
-
-  protected scoreColumn: string
-
-  public static capabilities = ['getFeatures', 'getRefNames']
-
-  public constructor(
-    config: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    const bedGzLoc = this.getConf('bedGzLocation') as FileLocation
-    const type = this.getConf(['index', 'indexType'])
-    const loc = this.getConf(['index', 'location'])
-    const autoSql = this.getConf('autoSql')
-    const pm = this.pluginManager
-
-    this.bed = new TabixIndexedFile({
-      filehandle: openLocation(bedGzLoc, pm),
-      csiFilehandle: type === 'CSI' ? openLocation(loc, pm) : undefined,
-      tbiFilehandle: type !== 'CSI' ? openLocation(loc, pm) : undefined,
-      chunkCacheSize: 50 * 2 ** 20,
-    })
-    this.columnNames = this.getConf('columnNames')
-    this.scoreColumn = this.getConf('scoreColumn')
-    this.parser = new BED({ autoSql })
-  }
-
-  public async getRefNames(opts: BaseOptions = {}) {
-    return this.bed.getReferenceSequenceNames(opts)
-  }
-
-  async getHeader() {
-    return this.bed.getHeader()
-  }
-
-  async getNames() {
-    if (this.columnNames.length) {
-      return this.columnNames
-    }
-    const header = await this.bed.getHeader()
-    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(f => f.trim())
-      : undefined
-  }
-
-  public getFeatures(query: Region, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      const meta = await this.bed.getMetadata()
-      const { columnNumbers } = meta
-      const colRef = columnNumbers.ref - 1
-      const colStart = columnNumbers.start - 1
-      const colEnd = columnNumbers.end - 1
-      // colSame handles special case for tabix where a single column is both
-      // the start and end, this is assumed to be covering the base at this
-      // position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same
-      const names = await this.getNames()
-      await this.bed.getLines(query.refName, query.start, query.end, {
-        lineCallback: (line, fileOffset) => {
-          observer.next(
-            featureData(
-              line,
-              colRef,
-              colStart,
-              colEnd,
-              this.scoreColumn,
-              this.parser,
-              `${this.id}-${fileOffset}`,
-              names,
-            ),
-          )
-        },
-        signal: opts.signal,
-      })
-      observer.complete()
-    }, opts.signal)
-  }
-
-  public freeResources(): void {}
-}