@jbrowse/plugin-variants 1.7.11 → 2.1.0

package/dist/VcfAdapter/VcfAdapter.js

@@ -1,383 +1,243 @@
 "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 _io = require("@jbrowse/core/util/io");
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _intervalTree = _interopRequireDefault(require("@flatten-js/interval-tree"));
-
-var _bgzfFilehandle = require("@gmod/bgzf-filehandle");
-
-var _vcf = _interopRequireDefault(require("@gmod/vcf"));
-
-var _VcfFeature = _interopRequireDefault(require("../VcfTabixAdapter/VcfFeature"));
-
-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 readVcf = function readVcf(f) {
-  var lines = f.split('\n');
-  var header = [];
-  var rest = [];
-  lines.forEach(function (line) {
-    if (line.startsWith('#')) {
-      header.push(line);
-    } else if (line) {
-      rest.push(line);
+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 __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
     }
-  });
-  return {
-    header: header.join('\n'),
-    lines: rest
-  };
+    return ar;
+};
+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 configuration_1 = require("@jbrowse/core/configuration");
+var interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+var bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
+var vcf_1 = __importDefault(require("@gmod/vcf"));
+var VcfFeature_1 = __importDefault(require("../VcfTabixAdapter/VcfFeature"));
+var readVcf = function (f) {
+    var lines = f.split('\n');
+    var header = [];
+    var rest = [];
+    lines.forEach(function (line) {
+        if (line.startsWith('#')) {
+            header.push(line);
+        }
+        else if (line) {
+            rest.push(line);
+        }
+    });
+    return { header: header.join('\n'), lines: rest };
 };
-
 function isGzip(buf) {
-  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
 }
-
-var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  (0, _inherits2.default)(VcfAdapter, _BaseFeatureDataAdapt);
-
-  var _super = _createSuper(VcfAdapter);
-
-  function VcfAdapter() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, VcfAdapter);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+var VcfAdapter = /** @class */ (function (_super) {
+    __extends(VcfAdapter, _super);
+    function VcfAdapter() {
+        return _super !== null && _super.apply(this, arguments) || this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "vcfFeatures", void 0);
-    return _this;
-  }
-
-  (0, _createClass2.default)(VcfAdapter, [{
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var _yield$this$setup, header;
-
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.setup();
-
-              case 2:
-                _yield$this$setup = _context.sent;
-                header = _yield$this$setup.header;
-                return _context.abrupt("return", header);
-
-              case 5:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getHeader() {
-        return _getHeader.apply(this, arguments);
-      }
-
-      return getHeader;
-    }()
-  }, {
-    key: "getMetadata",
-    value: function () {
-      var _getMetadata = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        var _yield$this$setup2, header, parser;
-
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.setup();
-
-              case 2:
-                _yield$this$setup2 = _context2.sent;
-                header = _yield$this$setup2.header;
-                parser = new _vcf.default({
-                  header: header
-                });
-                return _context2.abrupt("return", parser.getMetadata());
-
-              case 6:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getMetadata() {
-        return _getMetadata.apply(this, arguments);
-      }
-
-      return getMetadata;
-    }() // converts lines into an interval tree
-
-  }, {
-    key: "setupP",
-    value: function () {
-      var _setupP = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-        var buffer, buf, str, _readVcf, header, lines, intervalTree;
-
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return (0, _io.openLocation)((0, _configuration.readConfObject)(this.config, 'vcfLocation'), this.pluginManager).readFile();
-
-              case 2:
-                buffer = _context3.sent;
-
-                if (!isGzip(buffer)) {
-                  _context3.next = 9;
-                  break;
+    VcfAdapter.prototype.getHeader = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var header;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.setup()];
+                    case 1:
+                        header = (_a.sent()).header;
+                        return [2 /*return*/, header];
                 }
-
-                _context3.next = 6;
-                return (0, _bgzfFilehandle.unzip)(buffer);
-
-              case 6:
-                _context3.t0 = _context3.sent;
-                _context3.next = 10;
-                break;
-
-              case 9:
-                _context3.t0 = buffer;
-
-              case 10:
-                buf = _context3.t0;
-
-                if (!(buf.length > 536870888)) {
-                  _context3.next = 13;
-                  break;
+            });
+        });
+    };
+    VcfAdapter.prototype.getMetadata = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var header, parser;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.setup()];
+                    case 1:
+                        header = (_a.sent()).header;
+                        parser = new vcf_1.default({ header: header });
+                        return [2 /*return*/, parser.getMetadata()];
                 }
-
-                throw new Error('Data exceeds maximum string length (512MB)');
-
-              case 13:
-                str = new TextDecoder().decode(buf);
-                _readVcf = readVcf(str), header = _readVcf.header, lines = _readVcf.lines;
-                intervalTree = lines.map(function (line, id) {
-                  var _info$match;
-
-                  var _line$split = line.split('\t'),
-                      _line$split2 = (0, _slicedToArray2.default)(_line$split, 8),
-                      refName = _line$split2[0],
-                      startP = _line$split2[1],
-                      ref = _line$split2[3],
-                      info = _line$split2[7];
-
-                  var start = +startP - 1;
-                  var end = +(((_info$match = info.match(/END=(\d+)/)) === null || _info$match === void 0 ? void 0 : _info$match[1].trim()) || start + ref.length);
-                  return {
-                    line: line,
-                    refName: refName,
-                    start: start,
-                    end: end,
-                    id: id
-                  };
-                }).reduce(function (acc, obj) {
-                  var key = obj.refName;
-
-                  if (!acc[key]) {
-                    acc[key] = new _intervalTree.default();
-                  }
-
-                  acc[key].insert([obj.start, obj.end], obj);
-                  return acc;
-                }, {});
-                return _context3.abrupt("return", {
-                  header: header,
-                  intervalTree: intervalTree
-                });
-
-              case 17:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function setupP() {
-        return _setupP.apply(this, arguments);
-      }
-
-      return setupP;
-    }()
-  }, {
-    key: "setup",
-    value: function () {
-      var _setup = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
-        var _this2 = this;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
+            });
+        });
+    };
+    // converts lines into an interval tree
+    VcfAdapter.prototype.setupP = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var buffer, buf, _a, str, _b, header, lines, intervalTree;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0: return [4 /*yield*/, (0, io_1.openLocation)((0, configuration_1.readConfObject)(this.config, 'vcfLocation'), this.pluginManager).readFile()];
+                    case 1:
+                        buffer = _c.sent();
+                        if (!isGzip(buffer)) return [3 /*break*/, 3];
+                        return [4 /*yield*/, (0, bgzf_filehandle_1.unzip)(buffer)];
+                    case 2:
+                        _a = _c.sent();
+                        return [3 /*break*/, 4];
+                    case 3:
+                        _a = buffer;
+                        _c.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)');
+                        }
+                        str = new TextDecoder().decode(buf);
+                        _b = readVcf(str), header = _b.header, lines = _b.lines;
+                        intervalTree = lines
+                            .map(function (line, id) {
+                            var _a;
+                            var _b = __read(line.split('\t'), 8), refName = _b[0], startP = _b[1], ref = _b[3], info = _b[7];
+                            var start = +startP - 1;
+                            var end = +(((_a = info.match(/END=(\d+)/)) === null || _a === void 0 ? void 0 : _a[1].trim()) || start + ref.length);
+                            return { line: line, refName: refName, start: start, end: end, id: id };
+                        })
+                            .reduce(function (acc, obj) {
+                            var key = obj.refName;
+                            if (!acc[key]) {
+                                acc[key] = new interval_tree_1.default();
+                            }
+                            acc[key].insert([obj.start, obj.end], obj);
+                            return acc;
+                        }, {});
+                        return [2 /*return*/, { header: header, intervalTree: intervalTree }];
+                }
+            });
+        });
+    };
+    VcfAdapter.prototype.setup = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
                 if (!this.vcfFeatures) {
-                  this.vcfFeatures = this.setupP().catch(function (e) {
-                    _this2.vcfFeatures = undefined;
-                    throw e;
-                  });
+                    this.vcfFeatures = this.setupP().catch(function (e) {
+                        _this.vcfFeatures = undefined;
+                        throw e;
+                    });
                 }
-
-                return _context4.abrupt("return", this.vcfFeatures);
-
-              case 2:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function setup() {
-        return _setup.apply(this, arguments);
-      }
-
-      return setup;
-    }()
-  }, {
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
-        var _,
-            _yield$this$setup3,
-            intervalTree,
-            _args5 = arguments;
-
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
-                _ = _args5.length > 0 && _args5[0] !== undefined ? _args5[0] : {};
-                _context5.next = 3;
-                return this.setup();
-
-              case 3:
-                _yield$this$setup3 = _context5.sent;
-                intervalTree = _yield$this$setup3.intervalTree;
-                return _context5.abrupt("return", Object.keys(intervalTree));
-
-              case 6:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(region) {
-      var _this3 = 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 _intervalTree$refName, start, end, refName, _yield$_this3$setup, header, intervalTree, parser;
-
-          return _regenerator.default.wrap(function _callee6$(_context6) {
-            while (1) {
-              switch (_context6.prev = _context6.next) {
-                case 0:
-                  _context6.prev = 0;
-                  start = region.start, end = region.end, refName = region.refName;
-                  _context6.next = 4;
-                  return _this3.setup();
-
-                case 4:
-                  _yield$_this3$setup = _context6.sent;
-                  header = _yield$_this3$setup.header;
-                  intervalTree = _yield$_this3$setup.intervalTree;
-                  parser = new _vcf.default({
-                    header: header
-                  });
-                  (_intervalTree$refName = intervalTree[refName]) === null || _intervalTree$refName === void 0 ? void 0 : _intervalTree$refName.search([start, end]).forEach(function (f) {
-                    return observer.next(new _VcfFeature.default({
-                      variant: parser.parseLine(f.line),
-                      parser: parser,
-                      id: "".concat(_this3.id, "-").concat(f.id)
-                    }));
-                  });
-                  observer.complete();
-                  _context6.next = 15;
-                  break;
-
-                case 12:
-                  _context6.prev = 12;
-                  _context6.t0 = _context6["catch"](0);
-                  observer.error(_context6.t0);
-
-                case 15:
-                case "end":
-                  return _context6.stop();
-              }
-            }
-          }, _callee6, null, [[0, 12]]);
-        }));
-
-        return function (_x) {
-          return _ref.apply(this, arguments);
-        };
-      }(), opts.signal);
-    }
-  }, {
-    key: "freeResources",
-    value: function freeResources() {}
-  }]);
-  return VcfAdapter;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
+                return [2 /*return*/, this.vcfFeatures];
+            });
+        });
+    };
+    VcfAdapter.prototype.getRefNames = function (_) {
+        if (_ === void 0) { _ = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var intervalTree;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.setup()];
+                    case 1:
+                        intervalTree = (_a.sent()).intervalTree;
+                        return [2 /*return*/, Object.keys(intervalTree)];
+                }
+            });
+        });
+    };
+    VcfAdapter.prototype.getFeatures = function (region, 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, _a, header, intervalTree, parser_1, e_1;
+            var _this = this;
+            var _b;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
+                    case 0:
+                        _c.trys.push([0, 2, , 3]);
+                        start = region.start, end = region.end, refName = region.refName;
+                        return [4 /*yield*/, this.setup()];
+                    case 1:
+                        _a = _c.sent(), header = _a.header, intervalTree = _a.intervalTree;
+                        parser_1 = new vcf_1.default({ header: header });
+                        (_b = intervalTree[refName]) === null || _b === void 0 ? void 0 : _b.search([start, end]).forEach(function (f) {
+                            return observer.next(new VcfFeature_1.default({
+                                variant: parser_1.parseLine(f.line),
+                                parser: parser_1,
+                                id: "".concat(_this.id, "-").concat(f.id),
+                            }));
+                        });
+                        observer.complete();
+                        return [3 /*break*/, 3];
+                    case 2:
+                        e_1 = _c.sent();
+                        observer.error(e_1);
+                        return [3 /*break*/, 3];
+                    case 3: return [2 /*return*/];
+                }
+            });
+        }); }, opts.signal);
+    };
+    VcfAdapter.prototype.freeResources = function () { };
+    VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
+    return VcfAdapter;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
 exports.default = VcfAdapter;
-(0, _defineProperty2.default)(VcfAdapter, "capabilities", ['getFeatures', 'getRefNames']);
+//# sourceMappingURL=VcfAdapter.js.map

package/dist/VcfAdapter/VcfAdapter.js.map

@@ -0,0 +1 @@
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