@jbrowse/plugin-bed 1.7.10 → 2.0.1

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

@@ -0,0 +1,121 @@
+#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.ts

@@ -4,15 +4,13 @@ import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { FileLocation, Region } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
+import { FileLocation, Region, Feature } from '@jbrowse/core/util'
 import { TabixIndexedFile } from '@gmod/tabix'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { ucscProcessedTranscript } from '../util'
+import { featureData } from '../util'
 import PluginManager from '@jbrowse/core/PluginManager'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
@@ -32,31 +30,20 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     pluginManager?: PluginManager,
   ) {
     super(config, getSubAdapter, pluginManager)
-    const bedGzLocation = readConfObject(
-      config,
-      'bedGzLocation',
-    ) as FileLocation
-    const index = readConfObject(config, 'index') as {
-      indexType?: string
-      location: FileLocation
-    }
-    const autoSql = readConfObject(config, 'autoSql') as string
-    const { location, indexType } = index
+    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(bedGzLocation, this.pluginManager),
-      csiFilehandle:
-        indexType === 'CSI'
-          ? openLocation(location, this.pluginManager)
-          : undefined,
-      tbiFilehandle:
-        indexType !== 'CSI'
-          ? openLocation(location, this.pluginManager)
-          : undefined,
+      filehandle: openLocation(bedGzLoc, pm),
+      csiFilehandle: type === 'CSI' ? openLocation(loc, pm) : undefined,
+      tbiFilehandle: type !== 'CSI' ? openLocation(loc, pm) : undefined,
       chunkCacheSize: 50 * 2 ** 20,
     })
-    this.columnNames = readConfObject(config, 'columnNames')
-    this.scoreColumn = readConfObject(config, 'scoreColumn')
+    this.columnNames = this.getConf('columnNames')
+    this.scoreColumn = this.getConf('scoreColumn')
     this.parser = new BED({ autoSql })
   }
 
@@ -68,10 +55,6 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     return this.bed.getHeader()
   }
 
-  defaultParser(fields: string[], line: string) {
-    return Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]))
-  }
-
   async getNames() {
     if (this.columnNames.length) {
       return this.columnNames
@@ -79,12 +62,12 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     const header = await this.bed.getHeader()
     const defs = header.split('\n').filter(f => !!f)
     const defline = defs[defs.length - 1]
-    return defline && defline.includes('\t')
+    return defline?.includes('\t')
       ? defline
           .slice(1)
           .split('\t')
-          .map(field => field.trim())
-      : null
+          .map(f => f.trim())
+      : undefined
   }
 
   public getFeatures(query: Region, opts: BaseOptions = {}) {
@@ -97,55 +80,21 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
       // 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 colSame = colStart === colEnd ? 1 : 0
       const names = await this.getNames()
       await this.bed.getLines(query.refName, query.start, query.end, {
-        lineCallback: (line: string, fileOffset: number) => {
-          const l = line.split('\t')
-          const refName = l[colRef]
-          const start = +l[colStart]
-
-          const end = +l[colEnd] + colSame
-          const uniqueId = `${this.id}-${fileOffset}`
-          const data = names
-            ? this.defaultParser(names, line)
-            : this.parser.parseLine(line, { uniqueId })
-
-          const { blockCount, blockSizes, blockStarts, chromStarts } = data
-
-          if (blockCount) {
-            const starts = chromStarts || blockStarts || []
-            const sizes = blockSizes
-            const blocksOffset = start
-            data.subfeatures = []
-
-            for (let b = 0; b < blockCount; b += 1) {
-              const bmin = (starts[b] || 0) + blocksOffset
-              const bmax = bmin + (sizes[b] || 0)
-              data.subfeatures.push({
-                uniqueId: `${uniqueId}-${b}`,
-                start: bmin,
-                end: bmax,
-                type: 'block',
-              })
-            }
-          }
-
-          if (this.scoreColumn) {
-            data.score = +data[this.scoreColumn]
-          }
-          delete data.chrom
-          delete data.chromStart
-          delete data.chromEnd
-          const f = new SimpleFeature({
-            ...data,
-            start,
-            end,
-            refName,
-            uniqueId,
-          })
-          const r = f.get('thickStart') ? ucscProcessedTranscript(f) : f
-          observer.next(r)
+        lineCallback: (line, fileOffset) => {
+          observer.next(
+            featureData(
+              line,
+              colRef,
+              colStart,
+              colEnd,
+              this.scoreColumn,
+              this.parser,
+              `${this.id}-${fileOffset}`,
+              names,
+            ),
+          )
         },
         signal: opts.signal,
       })

package/src/index.ts

@@ -3,12 +3,13 @@ import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { configSchema as bigBedAdapterConfigSchema } from './BigBedAdapter'
 import { configSchema as bedTabixAdapterConfigSchema } from './BedTabixAdapter'
+import { configSchema as bedAdapterConfigSchema } from './BedAdapter'
 import { FileLocation } from '@jbrowse/core/util/types'
 import {
+  getFileName,
   makeIndex,
   makeIndexType,
   AdapterGuesser,
-  getFileName,
 } from '@jbrowse/core/util/tracks'
 
 export default class BedPlugin extends Plugin {
@@ -59,6 +60,16 @@ export default class BedPlugin extends Plugin {
             import('./BedTabixAdapter/BedTabixAdapter').then(r => r.default),
         }),
     )
+
+    pluginManager.addAdapterType(
+      () =>
+        new AdapterType({
+          name: 'BedAdapter',
+          configSchema: bedAdapterConfigSchema,
+          getAdapterClass: () =>
+            import('./BedAdapter/BedAdapter').then(r => r.default),
+        }),
+    )
     pluginManager.addToExtensionPoint(
       'Core-guessAdapterForLocation',
       (adapterGuesser: AdapterGuesser) => {
@@ -85,5 +96,27 @@ export default class BedPlugin extends Plugin {
         }
       },
     )
+
+    pluginManager.addToExtensionPoint(
+      'Core-guessAdapterForLocation',
+      (adapterGuesser: AdapterGuesser) => {
+        return (
+          file: FileLocation,
+          index?: FileLocation,
+          adapterHint?: string,
+        ) => {
+          const regexGuess = /\.bed$/i
+          const adapterName = 'BedAdapter'
+          const fileName = getFileName(file)
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bedLocation: file,
+            }
+          }
+          return adapterGuesser(file, index, adapterHint)
+        }
+      },
+    )
   }
 }

package/src/util.ts

@@ -1,4 +1,5 @@
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
+import { SimpleFeature, Feature } from '@jbrowse/core/util'
+import BED from '@gmod/bed'
 
 export function ucscProcessedTranscript(feature: Feature) {
   const children = feature.children()
@@ -97,11 +98,9 @@ export function ucscProcessedTranscript(feature: Feature) {
       })
     }
   })
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  const newData: Record<string, any> = {}
-  feature.tags().forEach(tag => {
-    newData[tag] = feature.get(tag)
-  })
+  const newData = Object.fromEntries(
+    feature.tags().map(tag => [tag, feature.get(tag)]),
+  )
   newData.subfeatures = newChildren
   newData.type = 'mRNA'
   newData.uniqueId = feature.id()
@@ -120,3 +119,63 @@ export function ucscProcessedTranscript(feature: Feature) {
   })
   return newFeature
 }
+
+function defaultParser(fields: string[], line: string) {
+  return Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]))
+}
+
+export function featureData(
+  line: string,
+  colRef: number,
+  colStart: number,
+  colEnd: number,
+  scoreColumn: string,
+  parser: typeof BED,
+  uniqueId: string,
+  names?: string[],
+) {
+  const l = line.split('\t')
+  const refName = l[colRef]
+  const start = +l[colStart]
+  const colSame = colStart === colEnd ? 1 : 0
+
+  const end = +l[colEnd] + colSame
+  const data = names
+    ? defaultParser(names, line)
+    : parser.parseLine(line, { uniqueId })
+
+  const { blockCount, blockSizes, blockStarts, chromStarts } = data
+
+  if (blockCount) {
+    const starts = chromStarts || blockStarts || []
+    const sizes = blockSizes
+    const blocksOffset = start
+    data.subfeatures = []
+
+    for (let b = 0; b < blockCount; b += 1) {
+      const bmin = (starts[b] || 0) + blocksOffset
+      const bmax = bmin + (sizes[b] || 0)
+      data.subfeatures.push({
+        uniqueId: `${uniqueId}-${b}`,
+        start: bmin,
+        end: bmax,
+        type: 'block',
+      })
+    }
+  }
+
+  if (scoreColumn) {
+    data.score = +data[scoreColumn]
+  }
+  delete data.chrom
+  delete data.chromStart
+  delete data.chromEnd
+  const f = new SimpleFeature({
+    ...data,
+    start,
+    end,
+    refName,
+    uniqueId,
+  })
+  return f.get('thickStart') ? ucscProcessedTranscript(f) : f
+}

package/dist/BedTabixAdapter/BedTabixAdapter.test.js

@@ -1,276 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _operators = require("rxjs/operators");
-
-var _BedTabixAdapter = _interopRequireDefault(require("./BedTabixAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch features from volvox-bed12.bed.gz', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, features, featuresArray, featuresJsonArray;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          adapter = new _BedTabixAdapter.default(_configSchema.default.create({
-            bedGzLocation: {
-              localPath: require.resolve('./test_data/volvox-bed12.bed.gz'),
-              locationType: 'LocalPathLocation'
-            },
-            index: {
-              location: {
-                localPath: require.resolve('./test_data/volvox-bed12.bed.gz.tbi'),
-                locationType: 'LocalPathLocation'
-              }
-            }
-          }));
-          features = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 20000,
-            assemblyName: 'volvox'
-          });
-          _context.t0 = expect;
-          _context.next = 5;
-          return adapter.hasDataForRefName('ctgA');
-
-        case 5:
-          _context.t1 = _context.sent;
-          (0, _context.t0)(_context.t1).toBe(true);
-          _context.t2 = expect;
-          _context.next = 10;
-          return adapter.hasDataForRefName('ctgB');
-
-        case 10:
-          _context.t3 = _context.sent;
-          (0, _context.t2)(_context.t3).toBe(false);
-          _context.next = 14;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 14:
-          featuresArray = _context.sent;
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
-
-        case 17:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));
-test('adapter can fetch features from volvox.sort.bed.gz simple bed3', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var adapter, features, featuresArray, featuresJsonArray;
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          adapter = new _BedTabixAdapter.default(_configSchema.default.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'
-              }
-            }
-          }));
-          features = adapter.getFeatures({
-            refName: 'contigA',
-            start: 0,
-            end: 20000,
-            assemblyName: 'volvox'
-          });
-          _context2.t0 = expect;
-          _context2.next = 5;
-          return adapter.hasDataForRefName('contigA');
-
-        case 5:
-          _context2.t1 = _context2.sent;
-          (0, _context2.t0)(_context2.t1).toBe(true);
-          _context2.t2 = expect;
-          _context2.next = 10;
-          return adapter.hasDataForRefName('ctgB');
-
-        case 10:
-          _context2.t3 = _context2.sent;
-          (0, _context2.t2)(_context2.t3).toBe(false);
-          _context2.next = 14;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 14:
-          featuresArray = _context2.sent;
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
-
-        case 17:
-        case "end":
-          return _context2.stop();
-      }
-    }
-  }, _callee2);
-})));
-test('adapter can fetch features bed with autosql', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-  var adapter, features, featuresArray, featuresJsonArray;
-  return _regenerator.default.wrap(function _callee3$(_context3) {
-    while (1) {
-      switch (_context3.prev = _context3.next) {
-        case 0:
-          adapter = new _BedTabixAdapter.default(_configSchema.default.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\n\"somatic variants converted from MAF files obtained through the NCI GDC\"\n    (\n    string chrom;      \"Chromosome (or contig, scaffold, etc.)\"\n    uint   chromStart; \"Start position in chromosome\"\n    uint   chromEnd;   \"End position in chromosome\"\n    string name;       \"Name of item\"\n    uint   score;      \"Score from 0-1000\"\n    char[1] strand;    \"+ or -\"\n    uint thickStart;   \"Start of where display should be thick (start codon)\"\n    uint thickEnd;     \"End of where display should be thick (stop codon)\"\n    uint reserved;     \"Used as itemRgb as of 2004-11-22\"\n    int blockCount;    \"Number of blocks\"\n    int[blockCount] blockSizes; \"Comma separated list of block sizes\"\n    int[blockCount] chromStarts; \"Start positions relative to chromStart\"\n    string sampleCount;    \"Number of samples with this variant\"\n    string freq;                    \"Variant frequency\"\n    lstring Hugo_Symbol;            \"Hugo symbol\"\n    lstring Entrez_Gene_Id;         \"Entrez Gene Id\"\n    lstring Variant_Classification; \"Class of variant\"\n    lstring Variant_Type;           \"Type of variant\"\n    lstring Reference_Allele;       \"Reference allele\"\n    lstring Tumor_Seq_Allele1;      \"Tumor allele 1\"\n    lstring Tumor_Seq_Allele2;      \"Tumor allele 2\"\n    lstring dbSNP_RS;               \"dbSNP RS number\"\n    lstring dbSNP_Val_Status;       \"dbSNP validation status\"\n    lstring days_to_death;          \"Number of days till death\"\n    lstring cigarettes_per_day;     \"Number of cigarettes per day\"\n    lstring weight;                 \"Weight\"\n    lstring alcohol_history;        \"Any alcohol consumption?\"\n    lstring alcohol_intensity;      \"Frequency of alcohol consumption\"\n    lstring bmi;                    \"Body mass index\"\n    lstring years_smoked;           \"Number of years smoked\"\n    lstring height;                 \"Height\"\n    lstring gender;                 \"Gender\"\n    lstring project_id;             \"TCGA Project id\"\n    lstring ethnicity;              \"Ethnicity\"\n    lstring Tumor_Sample_Barcode;   \"Tumor sample barcode\"\n    lstring Matched_Norm_Sample_Barcode;  \"Matcheds normal sample barcode\"\n    lstring case_id;                \"Case ID number\"\n)"
-          }));
-          features = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 20000,
-            assemblyName: 'volvox'
-          });
-          _context3.t0 = expect;
-          _context3.next = 5;
-          return adapter.hasDataForRefName('ctgA');
-
-        case 5:
-          _context3.t1 = _context3.sent;
-          (0, _context3.t0)(_context3.t1).toBe(true);
-          _context3.t2 = expect;
-          _context3.next = 10;
-          return adapter.hasDataForRefName('ctgB');
-
-        case 10:
-          _context3.t3 = _context3.sent;
-          (0, _context3.t2)(_context3.t3).toBe(false);
-          _context3.next = 14;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 14:
-          featuresArray = _context3.sent;
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
-
-        case 17:
-        case "end":
-          return _context3.stop();
-      }
-    }
-  }, _callee3);
-})));
-test('adapter can fetch bed with header', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
-  var adapter, features, featuresArray, featuresJsonArray;
-  return _regenerator.default.wrap(function _callee4$(_context4) {
-    while (1) {
-      switch (_context4.prev = _context4.next) {
-        case 0:
-          adapter = new _BedTabixAdapter.default(_configSchema.default.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'
-              }
-            }
-          }));
-          features = adapter.getFeatures({
-            refName: 'contigA',
-            start: 0,
-            end: 20000,
-            assemblyName: 'volvox'
-          });
-          _context4.t0 = expect;
-          _context4.next = 5;
-          return adapter.hasDataForRefName('contigA');
-
-        case 5:
-          _context4.t1 = _context4.sent;
-          (0, _context4.t0)(_context4.t1).toBe(true);
-          _context4.t2 = expect;
-          _context4.next = 10;
-          return adapter.hasDataForRefName('ctgB');
-
-        case 10:
-          _context4.t3 = _context4.sent;
-          (0, _context4.t2)(_context4.t3).toBe(false);
-          _context4.next = 14;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 14:
-          featuresArray = _context4.sent;
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
-
-        case 17:
-        case "end":
-          return _context4.stop();
-      }
-    }
-  }, _callee4);
-})));
-test('adapter can use gwas header', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
-  var adapter, features, featuresArray, featuresJsonArray;
-  return _regenerator.default.wrap(function _callee5$(_context5) {
-    while (1) {
-      switch (_context5.prev = _context5.next) {
-        case 0:
-          adapter = new _BedTabixAdapter.default(_configSchema.default.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'
-              }
-            }
-          }));
-          features = adapter.getFeatures({
-            refName: '1',
-            start: 0,
-            end: 100000,
-            assemblyName: 'hg19'
-          });
-          _context5.next = 4;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 4:
-          featuresArray = _context5.sent;
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
-
-        case 7:
-        case "end":
-          return _context5.stop();
-      }
-    }
-  }, _callee5);
-})));