@jbrowse/plugin-bed 1.6.8 → 1.7.1

package/dist/BedTabixAdapter/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/BigBedAdapter/BigBedAdapter.d.ts

@@ -1,46 +1,46 @@
-import { BigBed } from '@gmod/bbi';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
-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?;
-    configurePre(opts?: BaseOptions): Promise<{
-        bigbed: BigBed;
-        header: any;
-        parser: Parser;
-    }>;
-    configure(opts?: BaseOptions): Promise<{
-        bigbed: BigBed;
-        header: any;
-        parser: Parser;
-    }>;
-    getRefNames(opts?: BaseOptions): Promise<string[]>;
-    getHeader(opts?: BaseOptions): Promise<{
-        version: any;
-        fileType: any;
-        autoSql: {};
-        fields: {
-            [k: string]: string;
-        };
-    }>;
-    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    freeResources(): void;
-}
-export {};
+import { BigBed } from '@gmod/bbi';
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Region } from '@jbrowse/core/util/types';
+import { Feature } from '@jbrowse/core/util/simpleFeature';
+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?;
+    configurePre(opts?: BaseOptions): Promise<{
+        bigbed: BigBed;
+        header: any;
+        parser: Parser;
+    }>;
+    configure(opts?: BaseOptions): Promise<{
+        bigbed: BigBed;
+        header: any;
+        parser: Parser;
+    }>;
+    getRefNames(opts?: BaseOptions): Promise<string[]>;
+    getHeader(opts?: BaseOptions): Promise<{
+        version: any;
+        fileType: any;
+        autoSql: {};
+        fields: {
+            [k: string]: string;
+        };
+    }>;
+    getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    freeResources(): void;
+}
+export {};

package/dist/BigBedAdapter/BigBedAdapter.js

@@ -0,0 +1,341 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+
+var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+
+var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+
+var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _bbi = require("@gmod/bbi");
+
+var _bed = _interopRequireDefault(require("@gmod/bed"));
+
+var _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _operators = require("rxjs/operators");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _util = require("../util");
+
+var _excluded = ["fields"],
+    _excluded2 = ["chromStart", "chromEnd", "chrom"];
+
+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; } }
+
+function isUCSC(f) {
+  return f.get('thickStart') && f.get('blockCount') && f.get('strand') !== 0;
+}
+
+var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2["default"])(BigBedAdapter, _BaseFeatureDataAdapt);
+
+  var _super = _createSuper(BigBedAdapter);
+
+  function BigBedAdapter() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, BigBedAdapter);
+
+    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
+      args[_key] = arguments[_key];
+    }
+
+    _this = _super.call.apply(_super, [this].concat(args));
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "cached", void 0);
+    return _this;
+  }
+
+  (0, _createClass2["default"])(BigBedAdapter, [{
+    key: "configurePre",
+    value: function () {
+      var _configurePre = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee(opts) {
+        var bigbed, header, parser;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                bigbed = new _bbi.BigBed({
+                  filehandle: (0, _io.openLocation)((0, _configuration.readConfObject)(this.config, 'bigBedLocation'), this.pluginManager)
+                });
+                _context.next = 3;
+                return bigbed.getHeader(opts);
+
+              case 3:
+                header = _context.sent;
+                parser = new _bed["default"]({
+                  autoSql: header.autoSql
+                });
+                return _context.abrupt("return", {
+                  bigbed: bigbed,
+                  header: header,
+                  parser: parser
+                });
+
+              case 6:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function configurePre(_x) {
+        return _configurePre.apply(this, arguments);
+      }
+
+      return configurePre;
+    }()
+  }, {
+    key: "configure",
+    value: function () {
+      var _configure = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2(opts) {
+        var _this2 = this;
+
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                if (!this.cached) {
+                  this.cached = this.configurePre(opts)["catch"](function (e) {
+                    _this2.cached = undefined;
+                    throw e;
+                  });
+                }
+
+                return _context2.abrupt("return", this.cached);
+
+              case 2:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function configure(_x2) {
+        return _configure.apply(this, arguments);
+      }
+
+      return configure;
+    }()
+  }, {
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3(opts) {
+        var _yield$this$configure, header;
+
+        return _regenerator["default"].wrap(function _callee3$(_context3) {
+          while (1) {
+            switch (_context3.prev = _context3.next) {
+              case 0:
+                _context3.next = 2;
+                return this.configure(opts);
+
+              case 2:
+                _yield$this$configure = _context3.sent;
+                header = _yield$this$configure.header;
+                return _context3.abrupt("return", Object.keys(header.refsByName));
+
+              case 5:
+              case "end":
+                return _context3.stop();
+            }
+          }
+        }, _callee3, this);
+      }));
+
+      function getRefNames(_x3) {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+  }, {
+    key: "getHeader",
+    value: function () {
+      var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(opts) {
+        var _yield$this$configure2, parser, header, version, fileType, _parser$autoSql, fields, rest;
+
+        return _regenerator["default"].wrap(function _callee4$(_context4) {
+          while (1) {
+            switch (_context4.prev = _context4.next) {
+              case 0:
+                _context4.next = 2;
+                return this.configure(opts);
+
+              case 2:
+                _yield$this$configure2 = _context4.sent;
+                parser = _yield$this$configure2.parser;
+                header = _yield$this$configure2.header;
+                version = header.version, fileType = header.fileType;
+                _parser$autoSql = parser.autoSql, fields = _parser$autoSql.fields, rest = (0, _objectWithoutProperties2["default"])(_parser$autoSql, _excluded);
+                return _context4.abrupt("return", {
+                  version: version,
+                  fileType: fileType,
+                  autoSql: _objectSpread({}, rest),
+                  fields: Object.fromEntries(fields.map(function (_ref) {
+                    var name = _ref.name,
+                        comment = _ref.comment;
+                    return [name, comment];
+                  }))
+                });
+
+              case 8:
+              case "end":
+                return _context4.stop();
+            }
+          }
+        }, _callee4, this);
+      }));
+
+      function getHeader(_x4) {
+        return _getHeader.apply(this, arguments);
+      }
+
+      return getHeader;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(region) {
+      var _this3 = this;
+
+      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
+      var refName = region.refName,
+          start = region.start,
+          end = region.end;
+      var signal = opts.signal;
+      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
+        var _ref2 = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee5(observer) {
+          var _yield$_this3$configu, parser, bigbed, ob;
+
+          return _regenerator["default"].wrap(function _callee5$(_context5) {
+            while (1) {
+              switch (_context5.prev = _context5.next) {
+                case 0:
+                  _context5.prev = 0;
+                  _context5.next = 3;
+                  return _this3.configure(opts);
+
+                case 3:
+                  _yield$_this3$configu = _context5.sent;
+                  parser = _yield$_this3$configu.parser;
+                  bigbed = _yield$_this3$configu.bigbed;
+                  _context5.next = 8;
+                  return bigbed.getFeatureStream(refName, start, end, {
+                    signal: signal,
+                    basesPerSpan: end - start
+                  });
+
+                case 8:
+                  ob = _context5.sent;
+                  ob.pipe((0, _operators.mergeAll)(), (0, _operators.map)(function (r) {
+                    var data = parser.parseLine("".concat(refName, "\t").concat(r.start, "\t").concat(r.end, "\t").concat(r.rest), {
+                      uniqueId: r.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 = r.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(r.uniqueId, "-").concat(b),
+                          start: bmin,
+                          end: bmax,
+                          type: 'block'
+                        });
+                      }
+                    }
+
+                    if (r.uniqueId === undefined) {
+                      throw new Error('invalid bbi feature');
+                    }
+
+                    var chromStart = data.chromStart,
+                        chromEnd = data.chromEnd,
+                        chrom = data.chrom,
+                        rest = (0, _objectWithoutProperties2["default"])(data, _excluded2);
+                    var f = new _simpleFeature["default"]({
+                      id: "".concat(_this3.id, "-").concat(r.uniqueId),
+                      data: _objectSpread(_objectSpread({}, rest), {}, {
+                        start: r.start,
+                        end: r.end,
+                        refName: refName
+                      })
+                    }); // collection of heuristics for suggesting that this feature
+                    // should be converted to a gene, CNV bigbed has many gene like
+                    // features including thickStart and blockCount but no strand
+
+                    return isUCSC(f) ? (0, _util.ucscProcessedTranscript)(f) : f;
+                  })).subscribe(observer);
+                  _context5.next = 15;
+                  break;
+
+                case 12:
+                  _context5.prev = 12;
+                  _context5.t0 = _context5["catch"](0);
+                  observer.error(_context5.t0);
+
+                case 15:
+                case "end":
+                  return _context5.stop();
+              }
+            }
+          }, _callee5, null, [[0, 12]]);
+        }));
+
+        return function (_x5) {
+          return _ref2.apply(this, arguments);
+        };
+      }(), opts.signal);
+    }
+  }, {
+    key: "freeResources",
+    value: function freeResources() {}
+  }]);
+  return BigBedAdapter;
+}(_BaseAdapter.BaseFeatureDataAdapter);
+
+exports["default"] = BigBedAdapter;

package/dist/BigBedAdapter/BigBedAdapter.test.js

@@ -0,0 +1,63 @@
+"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/BigBedAdapter/configSchema.d.ts

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

package/dist/BigBedAdapter/configSchema.js

@@ -0,0 +1,22 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('BigBedAdapter', {
+  bigBedLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/my.bb',
+      locationType: 'UriLocation'
+    }
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/BigBedAdapter/index.d.ts

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

package/dist/BigBedAdapter/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/declare.d.js

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

package/dist/index.d.ts

@@ -1,6 +1,6 @@
-import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-export default class BedPlugin extends Plugin {
-    name: string;
-    install(pluginManager: PluginManager): void;
-}
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class BedPlugin extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}