@jbrowse/plugin-bed 1.7.11 → 2.1.0

package/src/BedTabixAdapter/BedTabixAdapter.ts

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import BED from '@gmod/bed'
 import {
   BaseFeatureDataAdapter,
@@ -14,7 +13,7 @@ import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
-  private parser: any
+  private parser: BED
 
   protected bed: TabixIndexedFile
 

package/src/BigBedAdapter/BigBedAdapter.ts

@@ -17,20 +17,8 @@ function isUCSC(f: Feature) {
   return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0
 }
 
-interface BEDFeature {
-  chrom: string
-  chromStart: number
-  chromEnd: number
-  [key: string]: any
-}
-
-interface Parser {
-  parseLine: (line: string, opts: { uniqueId: string | number }) => BEDFeature
-  autoSql: { fields: { name: string; comment: string }[] }
-}
-
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
-  private cached?: Promise<{ bigbed: BigBed; header: any; parser: Parser }>
+  private cached?: Promise<{ bigbed: BigBed; header: any; parser: BED }>
 
   public async configurePre(opts?: BaseOptions) {
     const bigbed = new BigBed({
@@ -40,7 +28,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
       ),
     })
     const header = await bigbed.getHeader(opts)
-    const parser = new BED({ autoSql: header.autoSql }) as Parser
+    const parser = new BED({ autoSql: header.autoSql })
     return { bigbed, header, parser }
   }
 

package/src/util.ts

@@ -130,7 +130,7 @@ export function featureData(
   colStart: number,
   colEnd: number,
   scoreColumn: string,
-  parser: typeof BED,
+  parser: BED,
   uniqueId: string,
   names?: string[],
 ) {

package/dist/BedAdapter/BedAdapter.test.js

@@ -1,255 +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 _BedAdapter = _interopRequireDefault(require("./BedAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-var _webEncoding = require("web-encoding");
-
-if (!window.TextDecoder) {
-  window.TextDecoder = _webEncoding.TextDecoder;
-}
-
-test('adapter can fetch features from volvox-bed12.bed', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var adapter, features, featuresArray, featuresJsonArray;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          adapter = new _BedAdapter.default(_configSchema.default.create({
-            bedLocation: {
-              localPath: require.resolve('./test_data/volvox-bed12.bed'),
-              locationType: 'LocalPathLocation'
-            }
-          }));
-          features = adapter.getFeatures({
-            refName: 'ctgA',
-            start: 0,
-            end: 20000,
-            assemblyName: 'volvox'
-          });
-          _context.t0 = expect;
-          _context.next = 5;
-          return adapter.hasDataForRefName('ctgA');
-
-        case 5:
-          _context.t1 = _context.sent;
-          (0, _context.t0)(_context.t1).toBe(true);
-          _context.t2 = expect;
-          _context.next = 10;
-          return adapter.hasDataForRefName('ctgB');
-
-        case 10:
-          _context.t3 = _context.sent;
-          (0, _context.t2)(_context.t3).toBe(false);
-          _context.next = 14;
-          return features.pipe((0, _operators.toArray)()).toPromise();
-
-        case 14:
-          featuresArray = _context.sent;
-          featuresJsonArray = featuresArray.map(function (f) {
-            return f.toJSON();
-          });
-          expect(featuresJsonArray.slice(0, 10)).toMatchSnapshot();
-
-        case 17:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));
-test('adapter can fetch features from volvox.sort.bed simple bed3', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-  var adapter, features, featuresArray, featuresJsonArray;
-  return _regenerator.default.wrap(function _callee2$(_context2) {
-    while (1) {
-      switch (_context2.prev = _context2.next) {
-        case 0:
-          adapter = new _BedAdapter.default(_configSchema.default.create({
-            bedLocation: {
-              localPath: require.resolve('./test_data/volvox.sort.bed'),
-              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 _BedAdapter.default(_configSchema.default.create({
-            bedLocation: {
-              localPath: require.resolve('./test_data/volvox-autosql.bed'),
-              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 _BedAdapter.default(_configSchema.default.create({
-            bedLocation: {
-              localPath: require.resolve('./test_data/volvox.sort.with.header.bed'),
-              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 _BedAdapter.default(_configSchema.default.create({
-            bedLocation: {
-              localPath: require.resolve('./test_data/gwas.bed'),
-              locationType: 'LocalPathLocation'
-            },
-            colRef: 0,
-            colStart: 1,
-            colEnd: 1
-          }));
-          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);
-})));

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);
-})));

package/dist/BigBedAdapter/BigBedAdapter.test.js

@@ -1,63 +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 _BigBedAdapter = _interopRequireDefault(require("./BigBedAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch features from volvox.bb', /*#__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 _BigBedAdapter.default(_configSchema.default.create({
-            bigBedLocation: {
-              localPath: require.resolve('./test_data/volvox.bb'),
-              locationType: 'LocalPathLocation'
-            }
-          }));
-          features = adapter.getFeatures({
-            assemblyName: 'volvox',
-            refName: 'ctgA',
-            start: 0,
-            end: 20000
-          });
-          _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).toMatchSnapshot();
-
-        case 17:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));

package/dist/declare.d.js

@@ -1 +0,0 @@
-"use strict";

package/dist/index.test.js

@@ -1,24 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _PluginManager = _interopRequireDefault(require("@jbrowse/core/PluginManager"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _ = _interopRequireDefault(require("."));
-
-test('plugin in a stock JBrowse', function () {
-  console.warn = jest.fn();
-  var pluginManager = new _PluginManager.default([new _.default()]);
-  pluginManager.createPluggableElements();
-  pluginManager.configure();
-  expect(function () {
-    return pluginManager.addPlugin(new _.default());
-  }).toThrow(/JBrowse already configured, cannot add plugins/);
-  var BigBedAdapter = pluginManager.getAdapterType('BigBedAdapter');
-  var config = BigBedAdapter.configSchema.create({
-    type: 'BigBedAdapter'
-  });
-  expect((0, _mobxStateTree.getSnapshot)(config)).toMatchSnapshot();
-});

package/src/declare.d.ts

@@ -1 +0,0 @@
-declare module '@gmod/bed'