@jbrowse/plugin-variants 1.4.4 → 1.5.3

package/dist/plugin-variants.esm.js

@@ -8,7 +8,7 @@ import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
 import Plugin from '@jbrowse/core/Plugin';
 import { linearBasicDisplayConfigSchemaFactory, linearBasicDisplayModelFactory, BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import { baseChordDisplayConfig, BaseChordDisplayModel, BaseChordDisplayComponentFactory } from '@jbrowse/plugin-circular-view';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { getRpcSessionId, getFileName, makeIndex, makeIndexType } from '@jbrowse/core/util/tracks';
 import { getContainingView, getSession, isSessionModelWithWidgets, getContainingTrack, polarToCartesian } from '@jbrowse/core/util';
 import { types, getSnapshot, getEnv } from 'mobx-state-tree';
 import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
@@ -20,10 +20,11 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { TabixIndexedFile } from '@gmod/tabix';
+import IntervalTree from '@flatten-js/interval-tree';
 import { unzip } from '@gmod/bgzf-filehandle';
 import { Dialog, DialogTitle, IconButton, Divider, DialogContent, FormControlLabel, Checkbox, DialogActions, Button, Paper, Typography, TextField, Link } from '@material-ui/core';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
-import { DataGrid } from '@material-ui/data-grid';
+import { DataGrid } from '@mui/x-data-grid';
 import { FeatureDetails, BaseCard } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import { makeStyles } from '@material-ui/core/styles';
 import CloseIcon from '@material-ui/icons/Close';
@@ -230,6 +231,8 @@ function _assertThisInitialized(self) {
 function _possibleConstructorReturn(self, call) {
   if (call && (typeof call === "object" || typeof call === "function")) {
     return call;
+  } else if (call !== void 0) {
+    throw new TypeError("Derived constructors may only return object or undefined");
   }
 
   return _assertThisInitialized(self);
@@ -593,11 +596,9 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
 
 
     var IteratorPrototype = {};
-
-    IteratorPrototype[iteratorSymbol] = function () {
+    define(IteratorPrototype, iteratorSymbol, function () {
       return this;
-    };
-
+    });
     var getProto = Object.getPrototypeOf;
     var NativeIteratorPrototype = getProto && getProto(getProto(values([])));
 
@@ -608,8 +609,9 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
     }
 
     var Gp = GeneratorFunctionPrototype.prototype = Generator.prototype = Object.create(IteratorPrototype);
-    GeneratorFunction.prototype = Gp.constructor = GeneratorFunctionPrototype;
-    GeneratorFunctionPrototype.constructor = GeneratorFunction;
+    GeneratorFunction.prototype = GeneratorFunctionPrototype;
+    define(Gp, "constructor", GeneratorFunctionPrototype);
+    define(GeneratorFunctionPrototype, "constructor", GeneratorFunction);
     GeneratorFunction.displayName = define(GeneratorFunctionPrototype, toStringTagSymbol, "GeneratorFunction"); // Helper for defining the .next, .throw, and .return methods of the
     // Iterator interface in terms of a single ._invoke method.
 
@@ -714,11 +716,9 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
     }
 
     defineIteratorMethods(AsyncIterator.prototype);
-
-    AsyncIterator.prototype[asyncIteratorSymbol] = function () {
+    define(AsyncIterator.prototype, asyncIteratorSymbol, function () {
       return this;
-    };
-
+    });
     exports.AsyncIterator = AsyncIterator; // Note that simple async functions are implemented on top of
     // AsyncIterator objects; they just return a Promise for the value of
     // the final result produced by the iterator.
@@ -895,13 +895,12 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
     // object to not be returned from this call. This ensures that doesn't happen.
     // See https://github.com/facebook/regenerator/issues/274 for more details.
 
-    Gp[iteratorSymbol] = function () {
+    define(Gp, iteratorSymbol, function () {
       return this;
-    };
-
-    Gp.toString = function () {
+    });
+    define(Gp, "toString", function () {
       return "[object Generator]";
-    };
+    });
 
     function pushTryEntry(locs) {
       var entry = {
@@ -1213,14 +1212,19 @@ var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
   } catch (accidentalStrictMode) {
     // This module should not be running in strict mode, so the above
     // assignment should always work unless something is misconfigured. Just
-    // in case runtime.js accidentally runs in strict mode, we can escape
+    // in case runtime.js accidentally runs in strict mode, in modern engines
+    // we can explicitly access globalThis. In older engines we can escape
     // strict mode using a global Function call. This could conceivably fail
     // if a Content Security Policy forbids using Function, but in that case
     // the proper solution is to fix the accidental strict mode problem. If
     // you've misconfigured your bundler to force strict mode and applied a
     // CSP to forbid Function, and you're not willing to fix either of those
     // problems, please detail your unique predicament in a GitHub issue.
-    Function("r", "regeneratorRuntime = r")(runtime);
+    if (typeof globalThis === "object") {
+      globalThis.regeneratorRuntime = runtime;
+    } else {
+      Function("r", "regeneratorRuntime = r")(runtime);
+    }
   }
 });
 
@@ -1318,7 +1322,7 @@ var Chord = /*#__PURE__*/observer(function Chord(_ref) {
   var endPosition;
   var endBlock;
   var alt = (_feature$get = feature.get('ALT')) === null || _feature$get === void 0 ? void 0 : _feature$get[0];
-  var bnd = parseBreakend(alt);
+  var bnd = alt && parseBreakend(alt);
 
   if (bnd) {
     // VCF BND
@@ -1374,6 +1378,7 @@ var Chord = /*#__PURE__*/observer(function Chord(_ref) {
       onMouseOut: function onMouseOut(evt) {
         if (!selected) {
           evt.target.style.stroke = strokeColor;
+          evt.target.style.strokeWidth = 1;
         }
       }
     });
@@ -1517,7 +1522,8 @@ var vcfTabixAdapterConfigSchema = /*#__PURE__*/ConfigurationSchema('VcfTabixAdap
   vcfGzLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/my.vcf.gz'
+      uri: '/path/to/my.vcf.gz',
+      locationType: 'UriLocation'
     }
   },
   index: /*#__PURE__*/ConfigurationSchema('VcfIndex', {
@@ -1529,7 +1535,8 @@ var vcfTabixAdapterConfigSchema = /*#__PURE__*/ConfigurationSchema('VcfTabixAdap
     location: {
       type: 'fileLocation',
       defaultValue: {
-        uri: '/path/to/my.vcf.gz.tbi'
+        uri: '/path/to/my.vcf.gz.tbi',
+        locationType: 'UriLocation'
       }
     }
   })
@@ -1541,7 +1548,8 @@ var vcfAdapterConfigSchema = /*#__PURE__*/ConfigurationSchema('VcfAdapter', {
   vcfLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/my.vcf'
+      uri: '/path/to/my.vcf',
+      locationType: 'UriLocation'
     }
   }
 }, {
@@ -1810,6 +1818,36 @@ var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.vcf\.b?gz$/i;
+          var adapterName = 'VcfTabixAdapter';
+          var fileName = getFileName(file);
+          var indexName = index && getFileName(index);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              vcfGzLocation: file,
+              index: {
+                location: index || makeIndex(file, '.tbi'),
+                indexType: makeIndexType(indexName, 'CSI', 'TBI')
+              }
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'VcfTabixAdapter') {
+            return 'VariantTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'VcfAdapter',
@@ -1821,6 +1859,22 @@ var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.vcf$/i;
+          var adapterName = 'VcfAdapter';
+          var fileName = getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              vcfLocation: file
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
       pluginManager.addRendererType(function () {
         return pluginManager.jbrequire(ChordRendererConfigF);
       });
@@ -1891,12 +1945,12 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   vcfGzLocation = readConfObject(this.config, 'vcfGzLocation');
                   location = readConfObject(this.config, ['index', 'location']);
                   indexType = readConfObject(this.config, ['index', 'indexType']);
-                  filehandle = openLocation(vcfGzLocation);
+                  filehandle = openLocation(vcfGzLocation, this.pluginManager);
                   isCSI = indexType === 'CSI';
                   vcf = new TabixIndexedFile({
                     filehandle: filehandle,
-                    csiFilehandle: isCSI ? openLocation(location) : undefined,
-                    tbiFilehandle: !isCSI ? openLocation(location) : undefined,
+                    csiFilehandle: isCSI ? openLocation(location, this.pluginManager) : undefined,
+                    tbiFilehandle: !isCSI ? openLocation(location, this.pluginManager) : undefined,
                     chunkCacheSize: 50 * Math.pow(2, 20),
                     chunkSizeLimit: 1000000000
                   });
@@ -2228,9 +2282,9 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     }()
   }, {
     key: "freeResources",
-    value: function freeResources()
-    /* { region } */
-    {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return _default;
@@ -2244,12 +2298,9 @@ var VcfTabixAdapter = {
 var readVcf = function readVcf(f) {
   var lines = f.split('\n');
   var header = [];
-  var refNames = [];
   var rest = [];
   lines.forEach(function (line) {
-    if (line.startsWith('##contig')) {
-      refNames.push(line.split('##contig=<ID=')[1].split(',')[0]);
-    } else if (line.startsWith('#')) {
+    if (line.startsWith('#')) {
       header.push(line);
     } else if (line) {
       rest.push(line);
@@ -2257,60 +2308,44 @@ var readVcf = function readVcf(f) {
   });
   return {
     header: header.join('\n'),
-    lines: rest,
-    refNames: refNames
+    lines: rest
   };
 };
 
+function isGzip(buf) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
+
 var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   _inherits(VcfAdapter, _BaseFeatureDataAdapt);
 
   var _super = /*#__PURE__*/_createSuper(VcfAdapter);
 
-  function VcfAdapter(config) {
+  function VcfAdapter() {
     _classCallCheck(this, VcfAdapter);
 
-    return _super.call(this, config);
+    return _super.apply(this, arguments);
   }
 
   _createClass(VcfAdapter, [{
-    key: "decodeFileContents",
+    key: "getHeader",
     value: function () {
-      var _decodeFileContents = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee() {
-        var vcfLocation, fileContents;
+      var _getHeader = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee() {
+        var _yield$this$setup, header;
+
         return runtime_1.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
-                vcfLocation = readConfObject(this.config, 'vcfLocation');
-                _context.next = 3;
-                return openLocation(vcfLocation).readFile();
-
-              case 3:
-                fileContents = _context.sent;
-
-                if (!(typeof fileContents[0] === 'number' && fileContents[0] === 31 && typeof fileContents[1] === 'number' && fileContents[1] === 139 && typeof fileContents[2] === 'number' && fileContents[2] === 8)) {
-                  _context.next = 12;
-                  break;
-                }
-
-                _context.t0 = new TextDecoder();
-                _context.next = 8;
-                return unzip(fileContents);
+                _context.next = 2;
+                return this.setup();
 
-              case 8:
-                _context.t1 = _context.sent;
-                fileContents = _context.t0.decode.call(_context.t0, _context.t1);
-                _context.next = 13;
-                break;
-
-              case 12:
-                fileContents = fileContents.toString();
-
-              case 13:
-                return _context.abrupt("return", readVcf(fileContents));
+              case 2:
+                _yield$this$setup = _context.sent;
+                header = _yield$this$setup.header;
+                return _context.abrupt("return", header);
 
-              case 14:
+              case 5:
               case "end":
                 return _context.stop();
             }
@@ -2318,31 +2353,34 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
         }, _callee, this);
       }));
 
-      function decodeFileContents() {
-        return _decodeFileContents.apply(this, arguments);
+      function getHeader() {
+        return _getHeader.apply(this, arguments);
       }
 
-      return decodeFileContents;
+      return getHeader;
     }()
   }, {
-    key: "getHeader",
+    key: "getMetadata",
     value: function () {
-      var _getHeader = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee2() {
-        var _yield$this$decodeFil, header;
+      var _getMetadata = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee2() {
+        var _yield$this$setup2, header, parser;
 
         return runtime_1.wrap(function _callee2$(_context2) {
           while (1) {
             switch (_context2.prev = _context2.next) {
               case 0:
                 _context2.next = 2;
-                return this.decodeFileContents();
+                return this.setup();
 
               case 2:
-                _yield$this$decodeFil = _context2.sent;
-                header = _yield$this$decodeFil.header;
-                return _context2.abrupt("return", header);
+                _yield$this$setup2 = _context2.sent;
+                header = _yield$this$setup2.header;
+                parser = new VCF({
+                  header: header
+                });
+                return _context2.abrupt("return", parser.getMetadata());
 
-              case 5:
+              case 6:
               case "end":
                 return _context2.stop();
             }
@@ -2350,111 +2388,131 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
         }, _callee2, this);
       }));
 
-      function getHeader() {
-        return _getHeader.apply(this, arguments);
+      function getMetadata() {
+        return _getMetadata.apply(this, arguments);
       }
 
-      return getHeader;
-    }()
+      return getMetadata;
+    }() // converts lines into an interval tree
+
   }, {
-    key: "getMetadata",
+    key: "setupP",
     value: function () {
-      var _getMetadata = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3() {
-        var _yield$this$decodeFil2, header, parser;
+      var _setupP = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3() {
+        var buffer, buf, str, _readVcf, header, lines, intervalTree;
 
         return runtime_1.wrap(function _callee3$(_context3) {
           while (1) {
             switch (_context3.prev = _context3.next) {
               case 0:
                 _context3.next = 2;
-                return this.decodeFileContents();
+                return openLocation(readConfObject(this.config, 'vcfLocation'), this.pluginManager).readFile();
 
               case 2:
-                _yield$this$decodeFil2 = _context3.sent;
-                header = _yield$this$decodeFil2.header;
-                parser = new VCF({
-                  header: header
-                });
-                return _context3.abrupt("return", parser.getMetadata());
+                buffer = _context3.sent;
+
+                if (!isGzip(buffer)) {
+                  _context3.next = 9;
+                  break;
+                }
+
+                _context3.next = 6;
+                return unzip(buffer);
 
               case 6:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
+                _context3.t0 = _context3.sent;
+                _context3.next = 10;
+                break;
 
-      function getMetadata() {
-        return _getMetadata.apply(this, arguments);
-      }
+              case 9:
+                _context3.t0 = buffer;
 
-      return getMetadata;
-    }()
-  }, {
-    key: "getLines",
-    value: function () {
-      var _getLines = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee4() {
-        var _this = this;
+              case 10:
+                buf = _context3.t0;
 
-        var _yield$this$decodeFil3, header, lines, parser;
+                if (!(buf.length > 536870888)) {
+                  _context3.next = 13;
+                  break;
+                }
 
-        return runtime_1.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.decodeFileContents();
+                throw new Error('Data exceeds maximum string length (512MB)');
 
-              case 2:
-                _yield$this$decodeFil3 = _context4.sent;
-                header = _yield$this$decodeFil3.header;
-                lines = _yield$this$decodeFil3.lines;
-                parser = new VCF({
-                  header: header
+              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$split2 = _slicedToArray(_line$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();
+                  }
+
+                  acc[key].insert([obj.start, obj.end], obj);
+                  return acc;
+                }, {});
+                return _context3.abrupt("return", {
+                  header: header,
+                  intervalTree: intervalTree
                 });
-                return _context4.abrupt("return", lines.map(function (line, index) {
-                  return new VCFFeature({
-                    variant: parser.parseLine(line),
-                    parser: parser,
-                    id: "".concat(_this.id, "-vcf-").concat(index)
-                  });
-                }));
 
-              case 7:
+              case 17:
               case "end":
-                return _context4.stop();
+                return _context3.stop();
             }
           }
-        }, _callee4, this);
+        }, _callee3, this);
       }));
 
-      function getLines() {
-        return _getLines.apply(this, arguments);
+      function setupP() {
+        return _setupP.apply(this, arguments);
       }
 
-      return getLines;
+      return setupP;
     }()
   }, {
     key: "setup",
     value: function () {
-      var _setup = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee5() {
-        return runtime_1.wrap(function _callee5$(_context5) {
+      var _setup = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee4() {
+        var _this = this;
+
+        return runtime_1.wrap(function _callee4$(_context4) {
           while (1) {
-            switch (_context5.prev = _context5.next) {
+            switch (_context4.prev = _context4.next) {
               case 0:
-                if (!this.setupP) {
-                  this.setupP = this.getLines();
+                if (!this.vcfFeatures) {
+                  this.vcfFeatures = this.setupP()["catch"](function (e) {
+                    _this.vcfFeatures = undefined;
+                    throw e;
+                  });
                 }
 
-                return _context5.abrupt("return", this.setupP);
+                return _context4.abrupt("return", this.vcfFeatures);
 
               case 2:
               case "end":
-                return _context5.stop();
+                return _context4.stop();
             }
           }
-        }, _callee5, this);
+        }, _callee4, this);
       }));
 
       function setup() {
@@ -2466,28 +2524,28 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getRefNames",
     value: function () {
-      var _getRefNames = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee6() {
-        var _yield$this$decodeFil4,
-            refNames;
+      var _getRefNames = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee5() {
+        var _yield$this$setup3,
+            intervalTree;
 
-        return runtime_1.wrap(function _callee6$(_context6) {
+        return runtime_1.wrap(function _callee5$(_context5) {
           while (1) {
-            switch (_context6.prev = _context6.next) {
+            switch (_context5.prev = _context5.next) {
               case 0:
-                _context6.next = 3;
-                return this.decodeFileContents();
+                _context5.next = 3;
+                return this.setup();
 
               case 3:
-                _yield$this$decodeFil4 = _context6.sent;
-                refNames = _yield$this$decodeFil4.refNames;
-                return _context6.abrupt("return", refNames);
+                _yield$this$setup3 = _context5.sent;
+                intervalTree = _yield$this$setup3.intervalTree;
+                return _context5.abrupt("return", Object.keys(intervalTree));
 
               case 6:
               case "end":
-                return _context6.stop();
+                return _context5.stop();
             }
           }
-        }, _callee6, this);
+        }, _callee5, this);
       }));
 
       function getRefNames() {
@@ -2503,30 +2561,47 @@ var VcfAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
       return ObservableCreate( /*#__PURE__*/function () {
-        var _ref = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee7(observer) {
-          var feats;
-          return runtime_1.wrap(function _callee7$(_context7) {
+        var _ref = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee6(observer) {
+          var _intervalTree$refName, start, end, refName, _yield$_this2$setup, header, intervalTree, parser;
+
+          return runtime_1.wrap(function _callee6$(_context6) {
             while (1) {
-              switch (_context7.prev = _context7.next) {
+              switch (_context6.prev = _context6.next) {
                 case 0:
-                  _context7.next = 2;
+                  _context6.prev = 0;
+                  start = region.start, end = region.end, refName = region.refName;
+                  _context6.next = 4;
                   return _this2.setup();
 
-                case 2:
-                  feats = _context7.sent;
-                  feats.forEach(function (f) {
-                    if (f.get('refName') === region.refName && f.get('end') > region.start && f.get('start') < region.end) {
-                      observer.next(f);
-                    }
+                case 4:
+                  _yield$_this2$setup = _context6.sent;
+                  header = _yield$_this2$setup.header;
+                  intervalTree = _yield$_this2$setup.intervalTree;
+                  parser = new VCF({
+                    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({
+                      variant: parser.parseLine(f.line),
+                      parser: parser,
+                      id: "".concat(_this2.id, "-").concat(f.id)
+                    }));
                   });
                   observer.complete();
+                  _context6.next = 15;
+                  break;
 
-                case 5:
+                case 12:
+                  _context6.prev = 12;
+                  _context6.t0 = _context6["catch"](0);
+                  observer.error(_context6.t0);
+
+                case 15:
                 case "end":
-                  return _context7.stop();
+                  return _context6.stop();
               }
             }
-          }, _callee7);
+          }, _callee6, null, [[0, 12]]);
         }));
 
         return function (_x) {