@jbrowse/plugin-gtf 1.7.9 → 2.0.0

package/dist/GtfAdapter/GtfAdapter.js

@@ -1,369 +1,227 @@
 "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 _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 _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 _gtf = _interopRequireDefault(require("@gmod/gtf"));
-
-var _util = require("../util");
-
-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 __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var io_1 = require("@jbrowse/core/util/io");
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+var simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
+var bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+var gtf_1 = __importDefault(require("@gmod/gtf"));
+var util_1 = require("../util");
 function isGzip(buf) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+    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];
+var default_1 = /** @class */ (function (_super) {
+    __extends(default_1, _super);
+    function default_1() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.intervalTrees = {};
+        return _this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "gtfFeatures", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "intervalTrees", {});
-    return _this;
-  }
-
-  (0, _createClass2.default)(_default, [{
-    key: "loadDataP",
-    value: function () {
-      var _loadDataP = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var buffer, buf, data, lines, feats, i, refName;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return (0, _io.openLocation)(this.getConf('gtfLocation'), 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;
+    default_1.prototype.loadDataP = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var gtfLoc, buffer, buf, _a, data, lines, feats, i, line, tab, refName;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        gtfLoc = this.getConf('gtfLocation');
+                        return [4 /*yield*/, (0, io_1.openLocation)(gtfLoc, this.pluginManager).readFile(opts)];
+                    case 1:
+                        buffer = _b.sent();
+                        if (!isGzip(buffer)) return [3 /*break*/, 3];
+                        return [4 /*yield*/, (0, bgzf_filehandle_1.unzip)(buffer)];
+                    case 2:
+                        _a = _b.sent();
+                        return [3 /*break*/, 4];
+                    case 3:
+                        _a = buffer;
+                        _b.label = 4;
+                    case 4:
+                        buf = _a;
+                        // 512MB  max chrome string length is 512MB
+                        if (buf.length > 536870888) {
+                            throw new Error('Data exceeds maximum string length (512MB)');
+                        }
+                        data = new TextDecoder('utf8', { fatal: true }).decode(buf);
+                        lines = data.split('\n').filter(function (f) { return !!f && !f.startsWith('#'); });
+                        feats = {};
+                        for (i = 0; i < lines.length; i++) {
+                            line = lines[i];
+                            if (line.startsWith('#')) {
+                                continue;
+                            }
+                            tab = line.indexOf('\t');
+                            refName = line.slice(0, tab);
+                            if (!feats[refName]) {
+                                feats[refName] = [];
+                            }
+                            feats[refName].push(lines[i]);
+                        }
+                        return [2 /*return*/, { feats: feats }];
                 }
-
-                throw new Error('Data exceeds maximum string length (512MB)');
-
-              case 13:
-                data = new TextDecoder('utf8', {
-                  fatal: true
-                }).decode(buf);
-                lines = data.split('\n').filter(function (f) {
-                  return !!f && !f.startsWith('#');
-                });
-                feats = {};
-
-                for (i = 0; i < lines.length; i++) {
-                  refName = lines[i].split('\t')[0];
-
-                  if (!feats[refName]) {
-                    feats[refName] = [];
-                  }
-
-                  feats[refName].push(lines[i]);
-                }
-
-                return _context.abrupt("return", {
-                  feats: feats
-                });
-
-              case 18:
-              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 _this2 = this;
-
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
+            });
+        });
+    };
+    default_1.prototype.loadData = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
                 if (!this.gtfFeatures) {
-                  this.gtfFeatures = this.loadDataP().catch(function (e) {
-                    _this2.gtfFeatures = undefined;
-                    throw e;
-                  });
+                    this.gtfFeatures = this.loadDataP(opts).catch(function (e) {
+                        _this.gtfFeatures = undefined;
+                        throw e;
+                    });
                 }
-
-                return _context2.abrupt("return", this.gtfFeatures);
-
-              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,
-            feats,
-            _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$loadData = _context3.sent;
-                feats = _yield$this$loadData.feats;
-                return _context3.abrupt("return", Object.keys(feats));
-
-              case 6:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "loadFeatureIntervalTreeHelper",
-    value: function () {
-      var _loadFeatureIntervalTreeHelper = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(refName) {
-        var _this3 = this;
-
-        var _yield$this$loadData2, feats, lines, data, intervalTree, ret, i, obj;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.loadData();
-
-              case 2:
-                _yield$this$loadData2 = _context4.sent;
-                feats = _yield$this$loadData2.feats;
-                lines = feats[refName];
-
-                if (lines) {
-                  _context4.next = 7;
-                  break;
+                return [2 /*return*/, this.gtfFeatures];
+            });
+        });
+    };
+    default_1.prototype.getRefNames = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var feats;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.loadData(opts)];
+                    case 1:
+                        feats = (_a.sent()).feats;
+                        return [2 /*return*/, Object.keys(feats)];
                 }
-
-                return _context4.abrupt("return", undefined);
-
-              case 7:
-                data = _gtf.default.parseStringSync(lines.join('\n'), {
-                  parseFeatures: true,
-                  parseComments: false,
-                  parseDirectives: false,
-                  parseSequences: false
-                });
-                intervalTree = new _intervalTree.default();
-                ret = data.flat().map(function (f, i) {
-                  return new _simpleFeature.default({
-                    data: (0, _util.featureData)(f),
-                    id: "".concat(_this3.id, "-offset-").concat(i)
-                  });
-                });
-
-                for (i = 0; i < ret.length; i++) {
-                  obj = ret[i];
-                  intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+            });
+        });
+    };
+    default_1.prototype.loadFeatureIntervalTreeHelper = function (refName) {
+        return __awaiter(this, void 0, void 0, function () {
+            var feats, lines, data, intervalTree, ret, i, obj;
+            var _this = this;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.loadData()];
+                    case 1:
+                        feats = (_a.sent()).feats;
+                        lines = feats[refName];
+                        if (!lines) {
+                            return [2 /*return*/, undefined];
+                        }
+                        data = gtf_1.default.parseStringSync(lines.join('\n'), {
+                            parseFeatures: true,
+                            parseComments: false,
+                            parseDirectives: false,
+                            parseSequences: false,
+                        });
+                        intervalTree = new interval_tree_1.default();
+                        ret = data.flat().map(function (f, i) {
+                            return new simpleFeature_1.default({
+                                data: (0, util_1.featureData)(f),
+                                id: "".concat(_this.id, "-").concat(refName, "-").concat(i),
+                            });
+                        });
+                        for (i = 0; i < ret.length; i++) {
+                            obj = ret[i];
+                            intervalTree.insert([obj.get('start'), obj.get('end')], obj);
+                        }
+                        return [2 /*return*/, intervalTree];
                 }
-
-                return _context4.abrupt("return", intervalTree);
-
-              case 12:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function loadFeatureIntervalTreeHelper(_x) {
-        return _loadFeatureIntervalTreeHelper.apply(this, arguments);
-      }
-
-      return loadFeatureIntervalTreeHelper;
-    }()
-  }, {
-    key: "loadFeatureIntervalTree",
-    value: function () {
-      var _loadFeatureIntervalTree = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(refName) {
-        var _this4 = this;
-
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
+            });
+        });
+    };
+    default_1.prototype.loadFeatureIntervalTree = function (refName) {
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
                 if (!this.intervalTrees[refName]) {
-                  this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(function (e) {
-                    _this4.intervalTrees[refName] = undefined;
-                    throw e;
-                  });
+                    this.intervalTrees[refName] = this.loadFeatureIntervalTreeHelper(refName).catch(function (e) {
+                        _this.intervalTrees[refName] = undefined;
+                        throw e;
+                    });
                 }
-
-                return _context5.abrupt("return", this.intervalTrees[refName]);
-
-              case 2:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function loadFeatureIntervalTree(_x2) {
-        return _loadFeatureIntervalTree.apply(this, arguments);
-      }
-
-      return loadFeatureIntervalTree;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(query) {
-      var _this5 = this;
-
-      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(observer) {
-          var start, end, refName, intervalTree;
-          return _regenerator.default.wrap(function _callee6$(_context6) {
-            while (1) {
-              switch (_context6.prev = _context6.next) {
-                case 0:
-                  _context6.prev = 0;
-                  start = query.start, end = query.end, refName = query.refName;
-                  _context6.next = 4;
-                  return _this5.loadFeatureIntervalTree(refName);
-
-                case 4:
-                  intervalTree = _context6.sent;
-                  intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(function (f) {
-                    return observer.next(f);
-                  });
-                  observer.complete();
-                  _context6.next = 12;
-                  break;
-
-                case 9:
-                  _context6.prev = 9;
-                  _context6.t0 = _context6["catch"](0);
-                  observer.error(_context6.t0);
-
-                case 12:
-                case "end":
-                  return _context6.stop();
-              }
-            }
-          }, _callee6, null, [[0, 9]]);
-        }));
-
-        return function (_x3) {
-          return _ref.apply(this, arguments);
-        };
-      }(), opts.signal);
-    }
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }]);
-  return _default;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
-exports.default = _default;
+                return [2 /*return*/, this.intervalTrees[refName]];
+            });
+        });
+    };
+    default_1.prototype.getFeatures = function (query, opts) {
+        var _this = this;
+        if (opts === void 0) { opts = {}; }
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var start, end, refName, intervalTree, e_1;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        _a.trys.push([0, 2, , 3]);
+                        start = query.start, end = query.end, refName = query.refName;
+                        return [4 /*yield*/, this.loadFeatureIntervalTree(refName)];
+                    case 1:
+                        intervalTree = _a.sent();
+                        intervalTree === null || intervalTree === void 0 ? void 0 : intervalTree.search([start, end]).forEach(function (f) { return observer.next(f); });
+                        observer.complete();
+                        return [3 /*break*/, 3];
+                    case 2:
+                        e_1 = _a.sent();
+                        observer.error(e_1);
+                        return [3 /*break*/, 3];
+                    case 3: return [2 /*return*/];
+                }
+            });
+        }); }, opts.signal);
+    };
+    default_1.prototype.freeResources = function ( /* { region } */) { };
+    return default_1;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = default_1;
+//# sourceMappingURL=GtfAdapter.js.map

package/dist/GtfAdapter/GtfAdapter.js.map

@@ -0,0 +1 @@
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package/dist/GtfAdapter/configSchema.js

@@ -1,22 +1,10 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('GtfAdapter', {
-  gtfLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/my.gtf',
-      locationType: 'UriLocation'
-    }
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('GtfAdapter', {
+    gtfLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/path/to/my.gtf', locationType: 'UriLocation' },
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/GtfAdapter/configSchema.js.map

@@ -0,0 +1 @@
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