@jbrowse/plugin-gff3 1.6.7 → 1.7.0

package/dist/Gff3Adapter/Gff3Adapter.js

@@ -0,0 +1,402 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+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 _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _io = require("@jbrowse/core/util/io");
+
+var _rxjs = require("@jbrowse/core/util/rxjs");
+
+var _intervalTree = _interopRequireDefault(require("@flatten-js/interval-tree"));
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+var _bgzfFilehandle = require("@gmod/bgzf-filehandle");
+
+var _gff = _interopRequireDefault(require("@gmod/gff"));
+
+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 isGzip(buf) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+
+var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2["default"])(_default, _BaseFeatureDataAdapt);
+
+  var _super = _createSuper(_default);
+
+  function _default() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+
+    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), "gffFeatures", void 0);
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "loadDataP",
+    value: function () {
+      var _loadDataP = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        var _this2 = this;
+
+        var buffer, buf, data, lines, headerLines, i, header, feats, intervalTree;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                _context.next = 2;
+                return (0, _io.openLocation)((0, _configuration.readConfObject)(this.config, 'gffLocation'), this.pluginManager).readFile();
+
+              case 2:
+                buffer = _context.sent;
+
+                if (!isGzip(buffer)) {
+                  _context.next = 9;
+                  break;
+                }
+
+                _context.next = 6;
+                return (0, _bgzfFilehandle.unzip)(buffer);
+
+              case 6:
+                _context.t0 = _context.sent;
+                _context.next = 10;
+                break;
+
+              case 9:
+                _context.t0 = buffer;
+
+              case 10:
+                buf = _context.t0;
+
+                if (!(buf.length > 536870888)) {
+                  _context.next = 13;
+                  break;
+                }
+
+                throw new Error('Data exceeds maximum string length (512MB)');
+
+              case 13:
+                data = new TextDecoder('utf8', {
+                  fatal: true
+                }).decode(buf);
+                lines = data.split('\n');
+                headerLines = [];
+
+                for (i = 0; i < lines.length && lines[i].startsWith('#'); i++) {
+                  headerLines.push(lines[i]);
+                }
+
+                header = headerLines.join('\n');
+                feats = _gff["default"].parseStringSync(data, {
+                  parseFeatures: true,
+                  parseComments: false,
+                  parseDirectives: false,
+                  parseSequences: false
+                });
+                intervalTree = feats.flat().map(function (f, i) {
+                  return new _simpleFeature["default"]({
+                    data: _this2.featureData(f),
+                    id: "".concat(_this2.id, "-offset-").concat(i)
+                  });
+                }).reduce(function (acc, obj) {
+                  var key = obj.get('refName');
+
+                  if (!acc[key]) {
+                    acc[key] = new _intervalTree["default"]();
+                  }
+
+                  acc[key].insert([obj.get('start'), obj.get('end')], obj);
+                  return acc;
+                }, {});
+                return _context.abrupt("return", {
+                  header: header,
+                  intervalTree: intervalTree
+                });
+
+              case 21:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function loadDataP() {
+        return _loadDataP.apply(this, arguments);
+      }
+
+      return loadDataP;
+    }()
+  }, {
+    key: "loadData",
+    value: function () {
+      var _loadData = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        var _this3 = this;
+
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                if (!this.gffFeatures) {
+                  this.gffFeatures = this.loadDataP()["catch"](function (e) {
+                    _this3.gffFeatures = undefined;
+                    throw e;
+                  });
+                }
+
+                return _context2.abrupt("return", this.gffFeatures);
+
+              case 2:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function loadData() {
+        return _loadData.apply(this, arguments);
+      }
+
+      return loadData;
+    }()
+  }, {
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee3() {
+        var opts,
+            _yield$this$loadData,
+            intervalTree,
+            _args3 = arguments;
+
+        return _regenerator["default"].wrap(function _callee3$(_context3) {
+          while (1) {
+            switch (_context3.prev = _context3.next) {
+              case 0:
+                opts = _args3.length > 0 && _args3[0] !== undefined ? _args3[0] : {};
+                _context3.next = 3;
+                return this.loadData();
+
+              case 3:
+                _yield$this$loadData = _context3.sent;
+                intervalTree = _yield$this$loadData.intervalTree;
+                return _context3.abrupt("return", Object.keys(intervalTree));
+
+              case 6:
+              case "end":
+                return _context3.stop();
+            }
+          }
+        }, _callee3, this);
+      }));
+
+      function getRefNames() {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+  }, {
+    key: "getHeader",
+    value: function () {
+      var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4() {
+        var _yield$this$loadData2, header;
+
+        return _regenerator["default"].wrap(function _callee4$(_context4) {
+          while (1) {
+            switch (_context4.prev = _context4.next) {
+              case 0:
+                _context4.next = 2;
+                return this.loadData();
+
+              case 2:
+                _yield$this$loadData2 = _context4.sent;
+                header = _yield$this$loadData2.header;
+                return _context4.abrupt("return", header);
+
+              case 5:
+              case "end":
+                return _context4.stop();
+            }
+          }
+        }, _callee4, this);
+      }));
+
+      function getHeader() {
+        return _getHeader.apply(this, arguments);
+      }
+
+      return getHeader;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(query) {
+      var _this4 = this;
+
+      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 _callee5(observer) {
+          var _intervalTree$refName, start, end, refName, _yield$_this4$loadDat, intervalTree;
+
+          return _regenerator["default"].wrap(function _callee5$(_context5) {
+            while (1) {
+              switch (_context5.prev = _context5.next) {
+                case 0:
+                  _context5.prev = 0;
+                  start = query.start, end = query.end, refName = query.refName;
+                  _context5.next = 4;
+                  return _this4.loadData();
+
+                case 4:
+                  _yield$_this4$loadDat = _context5.sent;
+                  intervalTree = _yield$_this4$loadDat.intervalTree;
+                  (_intervalTree$refName = intervalTree[refName]) === null || _intervalTree$refName === void 0 ? void 0 : _intervalTree$refName.search([start, end]).forEach(function (f) {
+                    return observer.next(f);
+                  });
+                  observer.complete();
+                  _context5.next = 13;
+                  break;
+
+                case 10:
+                  _context5.prev = 10;
+                  _context5.t0 = _context5["catch"](0);
+                  observer.error(_context5.t0);
+
+                case 13:
+                case "end":
+                  return _context5.stop();
+              }
+            }
+          }, _callee5, null, [[0, 10]]);
+        }));
+
+        return function (_x) {
+          return _ref.apply(this, arguments);
+        };
+      }(), opts.signal);
+    }
+  }, {
+    key: "featureData",
+    value: function featureData(data) {
+      var _this5 = this;
+
+      var f = _objectSpread({}, data);
+
+      f.start -= 1; // convert to interbase
+
+      if (data.strand === '+') {
+        f.strand = 1;
+      } else if (data.strand === '-') {
+        f.strand = -1;
+      } else if (data.strand === '.') {
+        f.strand = 0;
+      } else {
+        f.strand = undefined;
+      }
+
+      f.phase = Number(data.phase);
+      f.refName = data.seq_id;
+
+      if (data.score === null) {
+        delete f.score;
+      }
+
+      if (data.phase === null) {
+        delete f.score;
+      }
+
+      var defaultFields = ['start', 'end', 'seq_id', 'score', 'type', 'source', 'phase', 'strand'];
+      var dataAttributes = data.attributes || {};
+      Object.keys(dataAttributes).forEach(function (a) {
+        var b = a.toLowerCase();
+
+        if (defaultFields.includes(b)) {
+          // add "suffix" to tag name if it already exists
+          // reproduces behavior of NCList
+          b += '2';
+        }
+
+        if (dataAttributes[a] !== null) {
+          var attr = dataAttributes[a];
+
+          if (Array.isArray(attr) && attr.length === 1) {
+            ;
+            var _attr = attr;
+
+            var _attr2 = (0, _slicedToArray2["default"])(_attr, 1);
+
+            attr = _attr2[0];
+          }
+
+          f[b] = attr;
+        }
+      });
+      f.refName = f.seq_id; // the SimpleFeature constructor takes care of recursively inflating subfeatures
+
+      if (data.child_features && data.child_features.length) {
+        f.subfeatures = data.child_features.map(function (childLocs) {
+          return childLocs.map(function (childLoc) {
+            return _this5.featureData(childLoc);
+          });
+        }).flat();
+      }
+
+      delete f.child_features;
+      delete f.data;
+      delete f.derived_features;
+      delete f.attributes;
+      delete f.seq_id;
+      return f;
+    }
+  }, {
+    key: "freeResources",
+    value: function
+      /* { region } */
+    freeResources() {}
+  }]);
+  return _default;
+}(_BaseAdapter.BaseFeatureDataAdapter);
+
+exports["default"] = _default;

package/dist/Gff3Adapter/Gff3Adapter.test.js

@@ -0,0 +1,71 @@
+"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 _configSchema = _interopRequireDefault(require("./configSchema"));
+
+var _Gff3Adapter = _interopRequireDefault(require("./Gff3Adapter"));
+
+var _webEncoding = require("web-encoding");
+
+window.TextDecoder = _webEncoding.TextDecoder;
+describe('adapter can fetch features from volvox.gff3', function () {
+  var adapter;
+  beforeEach(function () {
+    adapter = new _Gff3Adapter["default"](_configSchema["default"].create({
+      gffLocation: {
+        localPath: require.resolve('../test_data/volvox.sort.gff3')
+      }
+    }));
+  });
+  it('test getfeatures on gff plain text adapter', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+    var features, featuresArray, featuresJsonArray;
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            features = adapter.getFeatures({
+              refName: 'ctgB',
+              start: 0,
+              end: 200000
+            });
+            _context.t0 = expect;
+            _context.next = 4;
+            return adapter.hasDataForRefName('ctgA');
+
+          case 4:
+            _context.t1 = _context.sent;
+            (0, _context.t0)(_context.t1).toBe(true);
+            _context.t2 = expect;
+            _context.next = 9;
+            return adapter.hasDataForRefName('ctgB');
+
+          case 9:
+            _context.t3 = _context.sent;
+            (0, _context.t2)(_context.t3).toBe(true);
+            _context.next = 13;
+            return features.pipe((0, _operators.toArray)()).toPromise();
+
+          case 13:
+            featuresArray = _context.sent;
+            // There are only 4 features in ctgB
+            expect(featuresArray.length).toBe(4);
+            featuresJsonArray = featuresArray.map(function (f) {
+              return f.toJSON();
+            });
+            expect(featuresJsonArray).toMatchSnapshot();
+
+          case 17:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  })));
+});

package/dist/Gff3Adapter/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)('Gff3Adapter', {
+  gffLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/my.gff',
+      locationType: 'UriLocation'
+    }
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/Gff3Adapter/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/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -0,0 +1,395 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+
+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 _BaseAdapter = require("@jbrowse/core/data_adapters/BaseAdapter");
+
+var _range = require("@jbrowse/core/util/range");
+
+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 _gff = _interopRequireDefault(require("@gmod/gff"));
+
+var _configuration = require("@jbrowse/core/configuration");
+
+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; } }
+
+var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
+  (0, _inherits2["default"])(_default, _BaseFeatureDataAdapt);
+
+  var _super = _createSuper(_default);
+
+  function _default(config, getSubAdapter, pluginManager) {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "gff", void 0);
+    (0, _defineProperty2["default"])((0, _assertThisInitialized2["default"])(_this), "dontRedispatch", void 0);
+    var gffGzLocation = (0, _configuration.readConfObject)(config, 'gffGzLocation');
+    var indexType = (0, _configuration.readConfObject)(config, ['index', 'indexType']);
+    var location = (0, _configuration.readConfObject)(config, ['index', 'location']);
+    var dontRedispatch = (0, _configuration.readConfObject)(config, 'dontRedispatch');
+    _this.dontRedispatch = dontRedispatch || ['chromosome', 'contig', 'region'];
+    _this.gff = new _tabix.TabixIndexedFile({
+      filehandle: (0, _io.openLocation)(gffGzLocation, _this.pluginManager),
+      csiFilehandle: indexType === 'CSI' ? (0, _io.openLocation)(location, _this.pluginManager) : undefined,
+      tbiFilehandle: indexType !== 'CSI' ? (0, _io.openLocation)(location, _this.pluginManager) : undefined,
+      chunkCacheSize: 50 * Math.pow(2, 20),
+      renameRefSeqs: function renameRefSeqs(n) {
+        return n;
+      }
+    });
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "getRefNames",
+    value: function () {
+      var _getRefNames = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+        var opts,
+            _args = arguments;
+        return _regenerator["default"].wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                opts = _args.length > 0 && _args[0] !== undefined ? _args[0] : {};
+                return _context.abrupt("return", this.gff.getReferenceSequenceNames(opts));
+
+              case 2:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function getRefNames() {
+        return _getRefNames.apply(this, arguments);
+      }
+
+      return getRefNames;
+    }()
+  }, {
+    key: "getHeader",
+    value: function () {
+      var _getHeader = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee2() {
+        return _regenerator["default"].wrap(function _callee2$(_context2) {
+          while (1) {
+            switch (_context2.prev = _context2.next) {
+              case 0:
+                return _context2.abrupt("return", this.gff.getHeader());
+
+              case 1:
+              case "end":
+                return _context2.stop();
+            }
+          }
+        }, _callee2, this);
+      }));
+
+      function getHeader() {
+        return _getHeader.apply(this, arguments);
+      }
+
+      return getHeader;
+    }()
+  }, {
+    key: "getFeatures",
+    value: function getFeatures(query) {
+      var _this2 = this;
+
+      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 _callee3(observer) {
+          var metadata;
+          return _regenerator["default"].wrap(function _callee3$(_context3) {
+            while (1) {
+              switch (_context3.prev = _context3.next) {
+                case 0:
+                  _context3.next = 2;
+                  return _this2.gff.getMetadata();
+
+                case 2:
+                  metadata = _context3.sent;
+
+                  _this2.getFeaturesHelper(query, opts, metadata, observer, true);
+
+                case 4:
+                case "end":
+                  return _context3.stop();
+              }
+            }
+          }, _callee3);
+        }));
+
+        return function (_x) {
+          return _ref.apply(this, arguments);
+        };
+      }(), opts.signal);
+    }
+  }, {
+    key: "getFeaturesHelper",
+    value: function () {
+      var _getFeaturesHelper = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee4(query) {
+        var _this3 = this;
+
+        var opts,
+            metadata,
+            observer,
+            allowRedispatch,
+            originalQuery,
+            lines,
+            minStart,
+            maxEnd,
+            gff3,
+            features,
+            _args4 = arguments;
+        return _regenerator["default"].wrap(function _callee4$(_context4) {
+          while (1) {
+            switch (_context4.prev = _context4.next) {
+              case 0:
+                opts = _args4.length > 1 && _args4[1] !== undefined ? _args4[1] : {};
+                metadata = _args4.length > 2 ? _args4[2] : undefined;
+                observer = _args4.length > 3 ? _args4[3] : undefined;
+                allowRedispatch = _args4.length > 4 ? _args4[4] : undefined;
+                originalQuery = _args4.length > 5 && _args4[5] !== undefined ? _args4[5] : query;
+                _context4.prev = 5;
+                lines = [];
+                _context4.next = 9;
+                return this.gff.getLines(query.refName, query.start, query.end, function (line, fileOffset) {
+                  lines.push(_this3.parseLine(metadata.columnNumbers, line, fileOffset));
+                });
+
+              case 9:
+                if (!(allowRedispatch && lines.length)) {
+                  _context4.next = 16;
+                  break;
+                }
+
+                minStart = Infinity;
+                maxEnd = -Infinity;
+                lines.forEach(function (line) {
+                  var featureType = line.fields[2]; // only expand redispatch range if feature is not a "dontRedispatch" type
+                  // skips large regions like chromosome,region
+
+                  if (!_this3.dontRedispatch.includes(featureType)) {
+                    var start = line.start - 1; // gff is 1-based
+
+                    if (start < minStart) {
+                      minStart = start;
+                    }
+
+                    if (line.end > maxEnd) {
+                      maxEnd = line.end;
+                    }
+                  }
+                });
+
+                if (!(maxEnd > query.end || minStart < query.start)) {
+                  _context4.next = 16;
+                  break;
+                }
+
+                // make a new feature callback to only return top-level features
+                // in the original query range
+                this.getFeaturesHelper(_objectSpread(_objectSpread({}, query), {}, {
+                  start: minStart,
+                  end: maxEnd
+                }), opts, metadata, observer, false, query);
+                return _context4.abrupt("return");
+
+              case 16:
+                gff3 = lines.map(function (lineRecord) {
+                  if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
+                    if (!lineRecord.fields[8].includes('_lineHash')) {
+                      lineRecord.fields[8] += ";_lineHash=".concat(lineRecord.lineHash);
+                    }
+                  } else {
+                    lineRecord.fields[8] = "_lineHash=".concat(lineRecord.lineHash);
+                  }
+
+                  return lineRecord.fields.join('\t');
+                }).join('\n');
+                features = _gff["default"].parseStringSync(gff3, {
+                  parseFeatures: true,
+                  parseComments: false,
+                  parseDirectives: false,
+                  parseSequences: false
+                });
+                features.forEach(function (featureLocs) {
+                  return _this3.formatFeatures(featureLocs).forEach(function (f) {
+                    if ((0, _range.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
+                      observer.next(f);
+                    }
+                  });
+                });
+                observer.complete();
+                _context4.next = 25;
+                break;
+
+              case 22:
+                _context4.prev = 22;
+                _context4.t0 = _context4["catch"](5);
+                observer.error(_context4.t0);
+
+              case 25:
+              case "end":
+                return _context4.stop();
+            }
+          }
+        }, _callee4, this, [[5, 22]]);
+      }));
+
+      function getFeaturesHelper(_x2) {
+        return _getFeaturesHelper.apply(this, arguments);
+      }
+
+      return getFeaturesHelper;
+    }()
+  }, {
+    key: "parseLine",
+    value: function parseLine(columnNumbers, line, fileOffset) {
+      var fields = line.split('\t'); // note: index column numbers are 1-based
+
+      return {
+        start: +fields[columnNumbers.start - 1],
+        end: +fields[columnNumbers.end - 1],
+        lineHash: fileOffset,
+        fields: fields
+      };
+    }
+  }, {
+    key: "formatFeatures",
+    value: function formatFeatures(featureLocs) {
+      var _this4 = this;
+
+      return featureLocs.map(function (featureLoc) {
+        return new _simpleFeature["default"]({
+          data: _this4.featureData(featureLoc),
+          // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+          id: "".concat(_this4.id, "-offset-").concat(featureLoc.attributes._lineHash[0])
+        });
+      });
+    }
+  }, {
+    key: "featureData",
+    value: function featureData(data) {
+      var _this5 = this;
+
+      var f = _objectSpread({}, data);
+
+      f.start -= 1; // convert to interbase
+
+      if (data.strand === '+') {
+        f.strand = 1;
+      } else if (data.strand === '-') {
+        f.strand = -1;
+      } else if (data.strand === '.') {
+        f.strand = 0;
+      } else {
+        f.strand = undefined;
+      }
+
+      f.phase = Number(data.phase);
+      f.refName = data.seq_id;
+
+      if (data.score === null) {
+        delete f.score;
+      }
+
+      if (data.phase === null) {
+        delete f.score;
+      }
+
+      var defaultFields = ['start', 'end', 'seq_id', 'score', 'type', 'source', 'phase', 'strand'];
+      var dataAttributes = data.attributes || {};
+      Object.keys(dataAttributes).forEach(function (a) {
+        var b = a.toLowerCase();
+
+        if (defaultFields.includes(b)) {
+          // add "suffix" to tag name if it already exists
+          // reproduces behavior of NCList
+          b += '2';
+        }
+
+        if (dataAttributes[a] !== null) {
+          var attr = dataAttributes[a];
+
+          if (Array.isArray(attr) && attr.length === 1) {
+            ;
+            var _attr = attr;
+
+            var _attr2 = (0, _slicedToArray2["default"])(_attr, 1);
+
+            attr = _attr2[0];
+          }
+
+          f[b] = attr;
+        }
+      });
+      f.refName = f.seq_id; // the SimpleFeature constructor takes care of recursively inflating subfeatures
+
+      if (data.child_features && data.child_features.length) {
+        f.subfeatures = data.child_features.map(function (childLocs) {
+          return childLocs.map(function (childLoc) {
+            return _this5.featureData(childLoc);
+          });
+        }).flat();
+      }
+
+      delete f.child_features;
+      delete f.data;
+      delete f.derived_features;
+      delete f._linehash;
+      delete f.attributes;
+      delete f.seq_id;
+      return f;
+    }
+  }, {
+    key: "freeResources",
+    value: function
+      /* { region } */
+    freeResources() {}
+  }]);
+  return _default;
+}(_BaseAdapter.BaseFeatureDataAdapter);
+
+exports["default"] = _default;

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.test.js

@@ -0,0 +1,74 @@
+"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 _configSchema = _interopRequireDefault(require("./configSchema"));
+
+var _Gff3TabixAdapter = _interopRequireDefault(require("./Gff3TabixAdapter"));
+
+describe('adapter can fetch features from volvox.gff3', function () {
+  var adapter;
+  beforeEach(function () {
+    adapter = new _Gff3TabixAdapter["default"](_configSchema["default"].create({
+      gffGzLocation: {
+        localPath: require.resolve('../test_data/volvox.sort.gff3.gz')
+      },
+      index: {
+        location: {
+          localPath: require.resolve('../test_data/volvox.sort.gff3.gz.tbi')
+        }
+      }
+    }));
+  });
+  it('test getfeatures on gff plain text adapter', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+    var features, featuresArray, featuresJsonArray;
+    return _regenerator["default"].wrap(function _callee$(_context) {
+      while (1) {
+        switch (_context.prev = _context.next) {
+          case 0:
+            features = adapter.getFeatures({
+              refName: 'ctgB',
+              start: 0,
+              end: 200000,
+              assemblyName: 'volvox'
+            });
+            _context.t0 = expect;
+            _context.next = 4;
+            return adapter.hasDataForRefName('ctgA');
+
+          case 4:
+            _context.t1 = _context.sent;
+            (0, _context.t0)(_context.t1).toBe(true);
+            _context.t2 = expect;
+            _context.next = 9;
+            return adapter.hasDataForRefName('ctgB');
+
+          case 9:
+            _context.t3 = _context.sent;
+            (0, _context.t2)(_context.t3).toBe(true);
+            _context.next = 13;
+            return features.pipe((0, _operators.toArray)()).toPromise();
+
+          case 13:
+            featuresArray = _context.sent;
+            // There are only 4 features in ctgB
+            expect(featuresArray.length).toBe(4);
+            featuresJsonArray = featuresArray.map(function (f) {
+              return f.toJSON();
+            });
+            expect(featuresJsonArray).toMatchSnapshot();
+
+          case 17:
+          case "end":
+            return _context.stop();
+        }
+      }
+    }, _callee);
+  })));
+});

package/dist/Gff3TabixAdapter/configSchema.js

@@ -0,0 +1,42 @@
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _default = (0, _configuration.ConfigurationSchema)('Gff3TabixAdapter', {
+  gffGzLocation: {
+    type: 'fileLocation',
+    defaultValue: {
+      uri: '/path/to/my.gff.gz',
+      locationType: 'UriLocation'
+    }
+  },
+  index: (0, _configuration.ConfigurationSchema)('Gff3TabixIndex', {
+    indexType: {
+      model: _mobxStateTree.types.enumeration('IndexType', ['TBI', 'CSI']),
+      type: 'stringEnum',
+      defaultValue: 'TBI'
+    },
+    location: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/my.gff.gz.tbi',
+        locationType: 'UriLocation'
+      }
+    }
+  }),
+  dontRedispatch: {
+    type: 'stringArray',
+    defaultValue: ['chromosome', 'region']
+  }
+}, {
+  explicitlyTyped: true
+});
+
+exports["default"] = _default;

package/dist/Gff3TabixAdapter/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/index.js

@@ -1,8 +1,138 @@
+"use strict";
 
-'use strict'
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-if (process.env.NODE_ENV === 'production') {
-  module.exports = require('./plugin-gff3.cjs.production.min.js')
-} else {
-  module.exports = require('./plugin-gff3.cjs.development.js')
-}
+var _typeof = require("@babel/runtime/helpers/typeof");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+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 _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+
+var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
+
+var _Gff3TabixAdapter = require("./Gff3TabixAdapter");
+
+var _tracks = require("@jbrowse/core/util/tracks");
+
+var _Gff3Adapter = require("./Gff3Adapter");
+
+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); }
+
+function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
+
+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; } }
+
+var _default = /*#__PURE__*/function (_Plugin) {
+  (0, _inherits2["default"])(_default, _Plugin);
+
+  var _super = _createSuper(_default);
+
+  function _default() {
+    var _this;
+
+    (0, _classCallCheck2["default"])(this, _default);
+
+    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), "name", 'GFF3Plugin');
+    return _this;
+  }
+
+  (0, _createClass2["default"])(_default, [{
+    key: "install",
+    value: function install(pluginManager) {
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'Gff3TabixAdapter',
+          configSchema: _Gff3TabixAdapter.configSchema,
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./Gff3TabixAdapter/Gff3TabixAdapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.gff3?\.b?gz$/i;
+          var adapterName = 'Gff3TabixAdapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var indexName = index && (0, _tracks.getFileName)(index);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bamLocation: file,
+              gffGzLocation: file,
+              index: {
+                location: index || (0, _tracks.makeIndex)(file, '.tbi'),
+                indexType: (0, _tracks.makeIndexType)(indexName, 'CSI', 'TBI')
+              }
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType["default"]({
+          name: 'Gff3Adapter',
+          configSchema: _Gff3Adapter.configSchema,
+          getAdapterClass: function getAdapterClass() {
+            return Promise.resolve().then(function () {
+              return _interopRequireWildcard(require('./Gff3Adapter/Gff3Adapter'));
+            }).then(function (r) {
+              return r["default"];
+            });
+          }
+        });
+      });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.gff3?$/i;
+          var adapterName = 'Gff3Adapter';
+          var fileName = (0, _tracks.getFileName)(file);
+          var obj = {
+            type: adapterName,
+            gffLocation: file
+          };
+
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+    }
+  }]);
+  return _default;
+}(_Plugin2["default"]);
+
+exports["default"] = _default;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "1.6.7",
+  "version": "1.7.0",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",
@@ -18,15 +18,12 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-gff3.esm.js",
-  "module": "dist/plugin-gff3.esm.js",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "start": "tsdx watch --verbose --noClean",
-    "build": "tsdx build",
+    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
     "test": "cd ../..; jest plugins/gff3 --passWithNoTests",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
@@ -54,5 +51,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "02012ec299c36647f755316571775d36b0fee5ec"
+  "gitHead": "cc13844074d11881d211342a6a7eea113561b70b"
 }