@jbrowse/plugin-bed 1.7.8 → 1.7.11

package/dist/BedAdapter/BedAdapter.test.js

@@ -0,0 +1,255 @@
+"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/BedAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/dist/BedAdapter/configSchema.js

@@ -0,0 +1,52 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.default = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('BedAdapter', {
+  bedLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/my.bed.gz',
+      locationType: 'UriLocation'
+    }
+  },
+  columnNames: {
+    type: 'stringArray',
+    description: 'List of column names',
+    defaultValue: []
+  },
+  scoreColumn: {
+    type: 'string',
+    description: 'The column to use as a "score" attribute',
+    defaultValue: ''
+  },
+  autoSql: {
+    type: 'string',
+    description: 'The autoSql definition for the data fields in the file',
+    defaultValue: ''
+  },
+  colRef: {
+    type: 'number',
+    description: 'The column to use as a "refName" attribute',
+    defaultValue: 0
+  },
+  colStart: {
+    type: 'number',
+    description: 'The column to use as a "start" attribute',
+    defaultValue: 1
+  },
+  colEnd: {
+    type: 'number',
+    description: 'The column to use as a "end" attribute',
+    defaultValue: 2
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports.default = _default;

package/dist/BedAdapter/index.d.ts

@@ -0,0 +1 @@
+export { default as configSchema } from './configSchema';

package/dist/BedAdapter/index.js

@@ -0,0 +1,15 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+Object.defineProperty(exports, "configSchema", {
+  enumerable: true,
+  get: function get() {
+    return _configSchema.default;
+  }
+});
+
+var _configSchema = _interopRequireDefault(require("./configSchema"));

package/dist/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -1,9 +1,8 @@
 import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Region, Feature } from '@jbrowse/core/util';
 import { TabixIndexedFile } from '@gmod/tabix';
 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 {
     private parser;
@@ -14,10 +13,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): Promise<any>;
     getHeader(): Promise<string>;
-    defaultParser(fields: string[], line: string): {
-        [k: string]: string;
-    };
-    getNames(): Promise<string[] | null>;
+    getNames(): Promise<string[] | undefined>;
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     freeResources(): void;
 }

package/dist/BedTabixAdapter/BedTabixAdapter.js

@@ -33,18 +33,10 @@ var _io = require("@jbrowse/core/util/io");
 
 var _rxjs = require("@jbrowse/core/util/rxjs");
 
-var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
-
 var _tabix = require("@gmod/tabix");
 
-var _configuration = require("@jbrowse/core/configuration");
-
 var _util = require("../util");
 
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
 function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
 
 function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
@@ -63,19 +55,24 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "bed", void 0);
     (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "columnNames", void 0);
     (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "scoreColumn", void 0);
-    var bedGzLocation = (0, _configuration.readConfObject)(config, 'bedGzLocation');
-    var index = (0, _configuration.readConfObject)(config, 'index');
-    var autoSql = (0, _configuration.readConfObject)(config, 'autoSql');
-    var location = index.location,
-        indexType = index.indexType;
+
+    var bedGzLoc = _this.getConf('bedGzLocation');
+
+    var type = _this.getConf(['index', 'indexType']);
+
+    var loc = _this.getConf(['index', 'location']);
+
+    var autoSql = _this.getConf('autoSql');
+
+    var pm = _this.pluginManager;
     _this.bed = new _tabix.TabixIndexedFile({
-      filehandle: (0, _io.openLocation)(bedGzLocation, _this.pluginManager),
-      csiFilehandle: indexType === 'CSI' ? (0, _io.openLocation)(location, _this.pluginManager) : undefined,
-      tbiFilehandle: indexType !== 'CSI' ? (0, _io.openLocation)(location, _this.pluginManager) : undefined,
+      filehandle: (0, _io.openLocation)(bedGzLoc, pm),
+      csiFilehandle: type === 'CSI' ? (0, _io.openLocation)(loc, pm) : undefined,
+      tbiFilehandle: type !== 'CSI' ? (0, _io.openLocation)(loc, pm) : undefined,
       chunkCacheSize: 50 * Math.pow(2, 20)
     });
-    _this.columnNames = (0, _configuration.readConfObject)(config, 'columnNames');
-    _this.scoreColumn = (0, _configuration.readConfObject)(config, 'scoreColumn');
+    _this.columnNames = _this.getConf('columnNames');
+    _this.scoreColumn = _this.getConf('scoreColumn');
     _this.parser = new _bed.default({
       autoSql: autoSql
     });
@@ -133,13 +130,6 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
       return getHeader;
     }()
-  }, {
-    key: "defaultParser",
-    value: function defaultParser(fields, line) {
-      return Object.fromEntries(line.split('\t').map(function (f, i) {
-        return [fields[i], f];
-      }));
-    }
   }, {
     key: "getNames",
     value: function () {
@@ -166,9 +156,9 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   return !!f;
                 });
                 defline = defs[defs.length - 1];
-                return _context3.abrupt("return", defline && defline.includes('\t') ? defline.slice(1).split('\t').map(function (field) {
-                  return field.trim();
-                }) : null);
+                return _context3.abrupt("return", defline !== null && defline !== void 0 && defline.includes('\t') ? defline.slice(1).split('\t').map(function (f) {
+                  return f.trim();
+                }) : undefined);
 
               case 8:
               case "end":
@@ -192,7 +182,7 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
       return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
         var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(observer) {
-          var meta, columnNumbers, colRef, colStart, colEnd, colSame, names;
+          var meta, columnNumbers, colRef, colStart, colEnd, names;
           return _regenerator.default.wrap(function _callee4$(_context4) {
             while (1) {
               switch (_context4.prev = _context4.next) {
@@ -209,69 +199,23 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   // 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
 
-                  colSame = colStart === colEnd ? 1 : 0;
-                  _context4.next = 10;
+                  _context4.next = 9;
                   return _this2.getNames();
 
-                case 10:
+                case 9:
                   names = _context4.sent;
-                  _context4.next = 13;
+                  _context4.next = 12;
                   return _this2.bed.getLines(query.refName, query.start, query.end, {
                     lineCallback: function lineCallback(line, fileOffset) {
-                      var l = line.split('\t');
-                      var refName = l[colRef];
-                      var start = +l[colStart];
-                      var end = +l[colEnd] + colSame;
-                      var uniqueId = "".concat(_this2.id, "-").concat(fileOffset);
-                      var data = names ? _this2.defaultParser(names, line) : _this2.parser.parseLine(line, {
-                        uniqueId: uniqueId
-                      });
-                      var blockCount = data.blockCount,
-                          blockSizes = data.blockSizes,
-                          blockStarts = data.blockStarts,
-                          chromStarts = data.chromStarts;
-
-                      if (blockCount) {
-                        var starts = chromStarts || blockStarts || [];
-                        var sizes = blockSizes;
-                        var blocksOffset = start;
-                        data.subfeatures = [];
-
-                        for (var b = 0; b < blockCount; b += 1) {
-                          var bmin = (starts[b] || 0) + blocksOffset;
-                          var bmax = bmin + (sizes[b] || 0);
-                          data.subfeatures.push({
-                            uniqueId: "".concat(uniqueId, "-").concat(b),
-                            start: bmin,
-                            end: bmax,
-                            type: 'block'
-                          });
-                        }
-                      }
-
-                      if (_this2.scoreColumn) {
-                        data.score = +data[_this2.scoreColumn];
-                      }
-
-                      delete data.chrom;
-                      delete data.chromStart;
-                      delete data.chromEnd;
-                      var f = new _simpleFeature.default(_objectSpread(_objectSpread({}, data), {}, {
-                        start: start,
-                        end: end,
-                        refName: refName,
-                        uniqueId: uniqueId
-                      }));
-                      var r = f.get('thickStart') ? (0, _util.ucscProcessedTranscript)(f) : f;
-                      observer.next(r);
+                      observer.next((0, _util.featureData)(line, colRef, colStart, colEnd, _this2.scoreColumn, _this2.parser, "".concat(_this2.id, "-").concat(fileOffset), names));
                     },
                     signal: opts.signal
                   });
 
-                case 13:
+                case 12:
                   observer.complete();
 
-                case 14:
+                case 13:
                 case "end":
                   return _context4.stop();
               }

package/dist/index.js

@@ -31,6 +31,8 @@ var _BigBedAdapter = require("./BigBedAdapter");
 
 var _BedTabixAdapter = require("./BedTabixAdapter");
 
+var _BedAdapter = require("./BedAdapter");
+
 var _tracks = require("@jbrowse/core/util/tracks");
 
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
@@ -108,6 +110,19 @@ var BedPlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType.default({
+          name: 'BedAdapter',
+          configSchema: _BedAdapter.configSchema,
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./BedAdapter/BedAdapter'));
+            }).then(function (r) {
+              return r.default;
+            });
+          }
+        });
+      });
       pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
         return function (file, index, adapterHint) {
           var regexGuess = /\.bed\.b?gz$/i;
@@ -126,6 +141,22 @@ var BedPlugin = /*#__PURE__*/function (_Plugin) {
             };
           }
 
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.bed$/i;
+          var adapterName = 'BedAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bedLocation: file
+            };
+          }
+
           return adapterGuesser(file, index, adapterHint);
         };
       });

package/dist/util.d.ts

@@ -1,2 +1,4 @@
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature';
+import { SimpleFeature, Feature } from '@jbrowse/core/util';
+import BED from '@gmod/bed';
 export declare function ucscProcessedTranscript(feature: Feature): Feature | SimpleFeature;
+export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: typeof BED, uniqueId: string, names?: string[]): Feature | SimpleFeature;