@jbrowse/plugin-variants 1.7.11 → 2.0.0

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -1,305 +1,199 @@
 "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 _get2 = _interopRequireDefault(require("@babel/runtime/helpers/get"));
-
-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 _util = require("@jbrowse/core/util");
-
-var _rxjs = require("@jbrowse/core/util/rxjs");
-
-var _tabix = require("@gmod/tabix");
-
-var _vcf = _interopRequireDefault(require("@gmod/vcf"));
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _VcfFeature = _interopRequireDefault(require("./VcfFeature"));
-
-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() {
-    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), "configured", void 0);
-    return _this;
-  }
-
-  (0, _createClass2.default)(_default, [{
-    key: "configurePre",
-    value: function () {
-      var _configurePre = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var vcfGzLocation, location, indexType, filehandle, isCSI, vcf, header;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                vcfGzLocation = (0, _configuration.readConfObject)(this.config, 'vcfGzLocation');
-                location = (0, _configuration.readConfObject)(this.config, ['index', 'location']);
-                indexType = (0, _configuration.readConfObject)(this.config, ['index', 'indexType']);
-                filehandle = (0, _io.openLocation)(vcfGzLocation, this.pluginManager);
-                isCSI = indexType === 'CSI';
-                vcf = new _tabix.TabixIndexedFile({
-                  filehandle: filehandle,
-                  csiFilehandle: isCSI ? (0, _io.openLocation)(location, this.pluginManager) : undefined,
-                  tbiFilehandle: !isCSI ? (0, _io.openLocation)(location, this.pluginManager) : undefined,
-                  chunkCacheSize: 50 * Math.pow(2, 20),
-                  chunkSizeLimit: 1000000000
-                });
-                _context.next = 8;
-                return vcf.getHeader();
-
-              case 8:
-                header = _context.sent;
-                return _context.abrupt("return", {
-                  filehandle: filehandle,
-                  vcf: vcf,
-                  parser: new _vcf.default({
-                    header: header
-                  })
-                });
-
-              case 10:
-              case "end":
-                return _context.stop();
+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 __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+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;
             }
-          }
-        }, _callee, this);
-      }));
-
-      function configurePre() {
-        return _configurePre.apply(this, arguments);
-      }
-
-      return configurePre;
-    }()
-  }, {
-    key: "configure",
-    value: function () {
-      var _configure = (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:
+            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 util_1 = require("@jbrowse/core/util");
+var rxjs_1 = require("@jbrowse/core/util/rxjs");
+var tabix_1 = require("@gmod/tabix");
+var vcf_1 = __importDefault(require("@gmod/vcf"));
+var configuration_1 = require("@jbrowse/core/configuration");
+var VcfFeature_1 = __importDefault(require("./VcfFeature"));
+var default_1 = /** @class */ (function (_super) {
+    __extends(default_1, _super);
+    function default_1() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    default_1.prototype.configurePre = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var vcfGzLocation, location, indexType, filehandle, isCSI, vcf, header;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        vcfGzLocation = (0, configuration_1.readConfObject)(this.config, 'vcfGzLocation');
+                        location = (0, configuration_1.readConfObject)(this.config, ['index', 'location']);
+                        indexType = (0, configuration_1.readConfObject)(this.config, ['index', 'indexType']);
+                        filehandle = (0, io_1.openLocation)(vcfGzLocation, this.pluginManager);
+                        isCSI = indexType === 'CSI';
+                        vcf = new tabix_1.TabixIndexedFile({
+                            filehandle: filehandle,
+                            csiFilehandle: isCSI
+                                ? (0, io_1.openLocation)(location, this.pluginManager)
+                                : undefined,
+                            tbiFilehandle: !isCSI
+                                ? (0, io_1.openLocation)(location, this.pluginManager)
+                                : undefined,
+                            chunkCacheSize: 50 * Math.pow(2, 20),
+                            chunkSizeLimit: 1000000000,
+                        });
+                        return [4 /*yield*/, vcf.getHeader()];
+                    case 1:
+                        header = _a.sent();
+                        return [2 /*return*/, {
+                                filehandle: filehandle,
+                                vcf: vcf,
+                                parser: new vcf_1.default({ header: header }),
+                            }];
+                }
+            });
+        });
+    };
+    default_1.prototype.configure = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var _this = this;
+            return __generator(this, function (_a) {
                 if (!this.configured) {
-                  this.configured = this.configurePre().catch(function (e) {
-                    _this2.configured = undefined;
-                    throw e;
-                  });
+                    this.configured = this.configurePre().catch(function (e) {
+                        _this.configured = undefined;
+                        throw e;
+                    });
                 }
-
-                return _context2.abrupt("return", this.configured);
-
-              case 2:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function configure() {
-        return _configure.apply(this, arguments);
-      }
-
-      return configure;
-    }()
-  }, {
-    key: "getRefNames",
-    value: function () {
-      var _getRefNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-        var opts,
-            _yield$this$configure,
-            vcf,
-            _args3 = arguments;
-
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                opts = _args3.length > 0 && _args3[0] !== undefined ? _args3[0] : {};
-                _context3.next = 3;
-                return this.configure();
-
-              case 3:
-                _yield$this$configure = _context3.sent;
-                vcf = _yield$this$configure.vcf;
-                return _context3.abrupt("return", vcf.getReferenceSequenceNames(opts));
-
-              case 6:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getRefNames() {
-        return _getRefNames.apply(this, arguments);
-      }
-
-      return getRefNames;
-    }()
-  }, {
-    key: "getHeader",
-    value: function () {
-      var _getHeader = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
-        var _yield$this$configure2, vcf;
-
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.configure();
-
-              case 2:
-                _yield$this$configure2 = _context4.sent;
-                vcf = _yield$this$configure2.vcf;
-                return _context4.abrupt("return", vcf.getHeader());
-
-              case 5:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function getHeader() {
-        return _getHeader.apply(this, arguments);
-      }
-
-      return getHeader;
-    }()
-  }, {
-    key: "getMetadata",
-    value: function () {
-      var _getMetadata = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
-        var _yield$this$configure3, parser;
-
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
-                _context5.next = 2;
-                return this.configure();
-
-              case 2:
-                _yield$this$configure3 = _context5.sent;
-                parser = _yield$this$configure3.parser;
-                return _context5.abrupt("return", parser.getMetadata());
-
-              case 5:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function getMetadata() {
-        return _getMetadata.apply(this, arguments);
-      }
-
-      return getMetadata;
-    }()
-  }, {
-    key: "getFeatures",
-    value: function getFeatures(query) {
-      var _this3 = this;
-
-      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(observer) {
-          var refName, start, end, _yield$_this3$configu, vcf, parser;
-
-          return _regenerator.default.wrap(function _callee6$(_context6) {
-            while (1) {
-              switch (_context6.prev = _context6.next) {
-                case 0:
-                  refName = query.refName, start = query.start, end = query.end;
-                  _context6.next = 3;
-                  return _this3.configure();
-
-                case 3:
-                  _yield$_this3$configu = _context6.sent;
-                  vcf = _yield$_this3$configu.vcf;
-                  parser = _yield$_this3$configu.parser;
-                  _context6.next = 8;
-                  return vcf.getLines(refName, start, end, _objectSpread({
-                    lineCallback: function lineCallback(line, fileOffset) {
-                      observer.next(new _VcfFeature.default({
-                        variant: parser.parseLine(line),
-                        parser: parser,
-                        id: "".concat(_this3.id, "-vcf-").concat(fileOffset)
-                      }));
-                    }
-                  }, opts));
-
-                case 8:
-                  observer.complete();
-
-                case 9:
-                case "end":
-                  return _context6.stop();
-              }
-            }
-          }, _callee6);
-        }));
-
-        return function (_x) {
-          return _ref.apply(this, arguments);
-        };
-      }(), opts.signal);
-    }
+                return [2 /*return*/, this.configured];
+            });
+        });
+    };
+    default_1.prototype.getRefNames = function (opts) {
+        if (opts === void 0) { opts = {}; }
+        return __awaiter(this, void 0, void 0, function () {
+            var vcf;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        vcf = (_a.sent()).vcf;
+                        return [2 /*return*/, vcf.getReferenceSequenceNames(opts)];
+                }
+            });
+        });
+    };
+    default_1.prototype.getHeader = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var vcf;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        vcf = (_a.sent()).vcf;
+                        return [2 /*return*/, vcf.getHeader()];
+                }
+            });
+        });
+    };
+    default_1.prototype.getMetadata = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var parser;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()];
+                    case 1:
+                        parser = (_a.sent()).parser;
+                        return [2 /*return*/, parser.getMetadata()];
+                }
+            });
+        });
+    };
+    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 refName, start, end, _a, vcf, parser;
+            var _this = this;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        refName = query.refName, start = query.start, end = query.end;
+                        return [4 /*yield*/, this.configure()];
+                    case 1:
+                        _a = _b.sent(), vcf = _a.vcf, parser = _a.parser;
+                        return [4 /*yield*/, vcf.getLines(refName, start, end, __assign({ lineCallback: function (line, fileOffset) {
+                                    observer.next(new VcfFeature_1.default({
+                                        variant: parser.parseLine(line),
+                                        parser: parser,
+                                        id: "".concat(_this.id, "-vcf-").concat(fileOffset),
+                                    }));
+                                } }, opts))];
+                    case 2:
+                        _b.sent();
+                        observer.complete();
+                        return [2 /*return*/];
+                }
+            });
+        }); }, opts.signal);
+    };
     /**
      * Checks if the data source has data for the given reference sequence,
      * and then gets the features in the region if it does
@@ -314,79 +208,48 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
      * @param opts - Feature adapter options
      * @returns Observable of Feature objects in the regions
      */
-
-  }, {
-    key: "getFeaturesInMultipleRegions",
-    value: function getFeaturesInMultipleRegions(regions) {
-      var _this4 = this;
-
-      var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
-      // TODO: restore commented version below once TSDX supports Rollup v2
-      // xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45
-      var superGetFeaturesInMultipleRegions = (0, _get2.default)((0, _getPrototypeOf2.default)(_default.prototype), "getFeaturesInMultipleRegions", this);
-      return (0, _rxjs.ObservableCreate)( /*#__PURE__*/function () {
-        var _ref2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(observer) {
-          var _yield$_this4$configu, vcf, bytes, _yield$_this4$configu2, filehandle, stat, pct;
-
-          return _regenerator.default.wrap(function _callee7$(_context7) {
-            while (1) {
-              switch (_context7.prev = _context7.next) {
-                case 0:
-                  _context7.next = 2;
-                  return _this4.configure();
-
-                case 2:
-                  _yield$_this4$configu = _context7.sent;
-                  vcf = _yield$_this4$configu.vcf;
-                  _context7.next = 6;
-                  return (0, _util.bytesForRegions)(regions, vcf.index);
-
-                case 6:
-                  bytes = _context7.sent;
-                  _context7.next = 9;
-                  return _this4.configure();
-
-                case 9:
-                  _yield$_this4$configu2 = _context7.sent;
-                  filehandle = _yield$_this4$configu2.filehandle;
-                  _context7.next = 13;
-                  return filehandle.stat();
-
-                case 13:
-                  stat = _context7.sent;
-                  pct = Math.round(bytes / stat.size * 100);
-
-                  if (pct > 100) {
-                    // this is just a bad estimate, make 100% if it goes over
-                    pct = 100;
-                  }
-
-                  if (pct > 60) {
-                    console.warn("getFeaturesInMultipleRegions fetching ".concat(pct, "% of VCF file, but whole-file streaming not yet implemented"));
-                  }
-
-                  superGetFeaturesInMultipleRegions.call(_this4, regions, opts).subscribe(observer); // super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
-
-                case 18:
-                case "end":
-                  return _context7.stop();
-              }
-            }
-          }, _callee7);
-        }));
-
-        return function (_x2) {
-          return _ref2.apply(this, arguments);
-        };
-      }());
-    }
-  }, {
-    key: "freeResources",
-    value: function
-      /* { region } */
-    freeResources() {}
-  }]);
-  return _default;
-}(_BaseAdapter.BaseFeatureDataAdapter);
-
-exports.default = _default;
+    default_1.prototype.getFeaturesInMultipleRegions = function (regions, opts) {
+        var _this = this;
+        if (opts === void 0) { opts = {}; }
+        // TODO: restore commented version below once TSDX supports Rollup v2
+        // xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45
+        var superGetFeaturesInMultipleRegions = _super.prototype.getFeaturesInMultipleRegions;
+        return (0, rxjs_1.ObservableCreate)(function (observer) { return __awaiter(_this, void 0, void 0, function () {
+            var vcf, bytes, filehandle, stat, pct;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.configure()
+                        // @ts-ignore
+                    ];
+                    case 1:
+                        vcf = (_a.sent()).vcf;
+                        return [4 /*yield*/, (0, util_1.bytesForRegions)(regions, vcf.index)];
+                    case 2:
+                        bytes = _a.sent();
+                        return [4 /*yield*/, this.configure()];
+                    case 3:
+                        filehandle = (_a.sent()).filehandle;
+                        return [4 /*yield*/, filehandle.stat()];
+                    case 4:
+                        stat = _a.sent();
+                        pct = Math.round((bytes / stat.size) * 100);
+                        if (pct > 100) {
+                            // this is just a bad estimate, make 100% if it goes over
+                            pct = 100;
+                        }
+                        if (pct > 60) {
+                            console.warn("getFeaturesInMultipleRegions fetching ".concat(pct, "% of VCF file, but whole-file streaming not yet implemented"));
+                        }
+                        superGetFeaturesInMultipleRegions
+                            .call(this, regions, opts)
+                            .subscribe(observer);
+                        return [2 /*return*/];
+                }
+            });
+        }); });
+    };
+    default_1.prototype.freeResources = function ( /* { region } */) { };
+    return default_1;
+}(BaseAdapter_1.BaseFeatureDataAdapter));
+exports.default = default_1;
+//# sourceMappingURL=VcfTabixAdapter.js.map

package/dist/VcfTabixAdapter/VcfTabixAdapter.js.map

@@ -0,0 +1 @@
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