@jbrowse/plugin-variants 1.5.0 → 1.5.4

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';
@@ -34,14 +34,9 @@ function ownKeys(object, enumerableOnly) {
 
   if (Object.getOwnPropertySymbols) {
     var symbols = Object.getOwnPropertySymbols(object);
-
-    if (enumerableOnly) {
-      symbols = symbols.filter(function (sym) {
-        return Object.getOwnPropertyDescriptor(object, sym).enumerable;
-      });
-    }
-
-    keys.push.apply(keys, symbols);
+    enumerableOnly && (symbols = symbols.filter(function (sym) {
+      return Object.getOwnPropertyDescriptor(object, sym).enumerable;
+    })), keys.push.apply(keys, symbols);
   }
 
   return keys;
@@ -49,19 +44,12 @@ function ownKeys(object, enumerableOnly) {
 
 function _objectSpread2(target) {
   for (var i = 1; i < arguments.length; i++) {
-    var source = arguments[i] != null ? arguments[i] : {};
-
-    if (i % 2) {
-      ownKeys(Object(source), true).forEach(function (key) {
-        _defineProperty(target, key, source[key]);
-      });
-    } else if (Object.getOwnPropertyDescriptors) {
-      Object.defineProperties(target, Object.getOwnPropertyDescriptors(source));
-    } else {
-      ownKeys(Object(source)).forEach(function (key) {
-        Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key));
-      });
-    }
+    var source = null != arguments[i] ? arguments[i] : {};
+    i % 2 ? ownKeys(Object(source), !0).forEach(function (key) {
+      _defineProperty(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;
@@ -122,6 +110,9 @@ function _defineProperties(target, props) {
 function _createClass(Constructor, protoProps, staticProps) {
   if (protoProps) _defineProperties(Constructor.prototype, protoProps);
   if (staticProps) _defineProperties(Constructor, staticProps);
+  Object.defineProperty(Constructor, "prototype", {
+    writable: false
+  });
   return Constructor;
 }
 
@@ -145,12 +136,15 @@ function _inherits(subClass, superClass) {
     throw new TypeError("Super expression must either be null or a function");
   }
 
-  subClass.prototype = Object.create(superClass && superClass.prototype, {
-    constructor: {
-      value: subClass,
-      writable: true,
-      configurable: true
-    }
+  Object.defineProperty(subClass, "prototype", {
+    value: Object.create(superClass && superClass.prototype, {
+      constructor: {
+        value: subClass,
+        writable: true,
+        configurable: true
+      }
+    }),
+    writable: false
   });
   if (superClass) _setPrototypeOf(subClass, superClass);
 }
@@ -266,7 +260,7 @@ function _superPropBase(object, property) {
   return object;
 }
 
-function _get(target, property, receiver) {
+function _get() {
   if (typeof Reflect !== "undefined" && Reflect.get) {
     _get = Reflect.get;
   } else {
@@ -277,14 +271,14 @@ function _get(target, property, receiver) {
       var desc = Object.getOwnPropertyDescriptor(base, property);
 
       if (desc.get) {
-        return desc.get.call(receiver);
+        return desc.get.call(arguments.length < 3 ? target : receiver);
       }
 
       return desc.value;
     };
   }
 
-  return _get(target, property, receiver || target);
+  return _get.apply(this, arguments);
 }
 
 function _slicedToArray(arr, i) {
@@ -1818,6 +1812,36 @@ var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.vcf\.b?gz$/i;
+          var adapterName = 'VcfTabixAdapter';
+          var fileName = getFileName(file);
+          var indexName = index && getFileName(index);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              vcfGzLocation: file,
+              index: {
+                location: index || makeIndex(file, '.tbi'),
+                indexType: makeIndexType(indexName, 'CSI', 'TBI')
+              }
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
+      pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', function (trackTypeGuesser) {
+        return function (adapterName) {
+          if (adapterName === 'VcfTabixAdapter') {
+            return 'VariantTrack';
+          }
+
+          return trackTypeGuesser(adapterName);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'VcfAdapter',
@@ -1829,6 +1853,22 @@ var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.vcf$/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);
       });
@@ -2236,7 +2276,9 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
     }()
   }, {
     key: "freeResources",
-    value: function freeResources() {}
+    value: function
+      /* { region } */
+    freeResources() {}
   }]);
 
   return _default;
@@ -2250,12 +2292,9 @@ 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);
@@ -2263,60 +2302,44 @@ 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, getSubAdapter, pluginManager) {
+  function VcfAdapter() {
     _classCallCheck(this, VcfAdapter);
 
-    return _super.call(this, config, getSubAdapter, pluginManager);
+    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, this.pluginManager).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();
             }
@@ -2324,31 +2347,34 @@ 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();
             }
@@ -2356,122 +2382,131 @@ 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.vcfFeatures) {
-                  this.vcfFeatures = this.getLines().then(function (feats) {
-                    return feats.reduce(function (acc, obj) {
-                      var key = obj.get('refName');
-
-                      if (!acc[key]) {
-                        acc[key] = new IntervalTree();
-                      }
-
-                      acc[key].insert([obj.get('start'), obj.get('end')], obj);
-                      return acc;
-                    }, {});
+                  this.vcfFeatures = this.setupP()["catch"](function (e) {
+                    _this.vcfFeatures = undefined;
+                    throw e;
                   });
                 }
 
-                return _context5.abrupt("return", this.vcfFeatures);
+                return _context4.abrupt("return", this.vcfFeatures);
 
               case 2:
               case "end":
-                return _context5.stop();
+                return _context4.stop();
             }
           }
-        }, _callee5, this);
+        }, _callee4, this);
       }));
 
       function setup() {
@@ -2483,28 +2518,28 @@ 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() {
@@ -2520,40 +2555,47 @@ 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 start, end, refName, vcfFeatures, tree, 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.prev = 0;
+                  _context6.prev = 0;
                   start = region.start, end = region.end, refName = region.refName;
-                  _context7.next = 4;
+                  _context6.next = 4;
                   return _this2.setup();
 
                 case 4:
-                  vcfFeatures = _context7.sent;
-                  tree = vcfFeatures[refName];
-                  feats = tree.search([start, end]); //  expected array ['val1']
-
-                  feats.forEach(function (f) {
-                    observer.next(f);
+                  _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();
-                  _context7.next = 14;
+                  _context6.next = 15;
                   break;
 
-                case 11:
-                  _context7.prev = 11;
-                  _context7.t0 = _context7["catch"](0);
-                  observer.error(_context7.t0);
+                case 12:
+                  _context6.prev = 12;
+                  _context6.t0 = _context6["catch"](0);
+                  observer.error(_context6.t0);
 
-                case 14:
+                case 15:
                 case "end":
-                  return _context7.stop();
+                  return _context6.stop();
               }
             }
-          }, _callee7, null, [[0, 11]]);
+          }, _callee6, null, [[0, 12]]);
         }));
 
         return function (_x) {
@@ -2846,7 +2888,9 @@ function VariantFeatureDetails(props) {
   }, props)), /*#__PURE__*/React.createElement(Divider, null), feat.type === 'breakend' ? /*#__PURE__*/React.createElement(BreakendPanel, {
     feature: feat,
     locStrings: feat.ALT.map(function (alt) {
-      return parseBreakend(alt).MatePosition;
+      var _parseBreakend;
+
+      return ((_parseBreakend = parseBreakend(alt)) === null || _parseBreakend === void 0 ? void 0 : _parseBreakend.MatePosition) || '';
     }),
     model: model
   }) : null, feat.type === 'translocation' ? /*#__PURE__*/React.createElement(BreakendPanel, {