@jbrowse/plugin-variants 1.5.6 → 1.6.0

package/dist/plugin-variants.esm.js

@@ -9,7 +9,7 @@ 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, getFileName, makeIndex, makeIndexType } from '@jbrowse/core/util/tracks';
-import { getContainingView, getSession, isSessionModelWithWidgets, getContainingTrack, polarToCartesian } from '@jbrowse/core/util';
+import { getContainingView, getSession, isSessionModelWithWidgets, getContainingTrack, polarToCartesian, bytesForRegions } from '@jbrowse/core/util';
 import { types, getSnapshot, getEnv } from 'mobx-state-tree';
 import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType';
 import { PropTypes as PropTypes$2, observer } from 'mobx-react';
@@ -136,14 +136,14 @@ 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);
@@ -1818,16 +1818,19 @@ var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
           var adapterName = 'VcfTabixAdapter';
           var fileName = getFileName(file);
           var indexName = index && getFileName(index);
+          var obj = {
+            type: adapterName,
+            vcfGzLocation: file,
+            index: {
+              location: index || makeIndex(file, '.tbi'),
+              indexType: makeIndexType(indexName, 'CSI', 'TBI')
+            }
+          };
 
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              vcfGzLocation: file,
-              index: {
-                location: index || makeIndex(file, '.tbi'),
-                indexType: makeIndexType(indexName, 'CSI', 'TBI')
-              }
-            };
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
           }
 
           return adapterGuesser(file, index, adapterHint);
@@ -1925,51 +1928,78 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }
 
   _createClass(_default, [{
+    key: "configurePre",
+    value: function () {
+      var _configurePre = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee() {
+        var vcfGzLocation, location, indexType, filehandle, isCSI, vcf, header;
+        return runtime_1.wrap(function _callee$(_context) {
+          while (1) {
+            switch (_context.prev = _context.next) {
+              case 0:
+                vcfGzLocation = readConfObject(this.config, 'vcfGzLocation');
+                location = readConfObject(this.config, ['index', 'location']);
+                indexType = readConfObject(this.config, ['index', 'indexType']);
+                filehandle = openLocation(vcfGzLocation, this.pluginManager);
+                isCSI = indexType === 'CSI';
+                vcf = new TabixIndexedFile({
+                  filehandle: filehandle,
+                  csiFilehandle: isCSI ? openLocation(location, this.pluginManager) : undefined,
+                  tbiFilehandle: !isCSI ? 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({
+                    header: header
+                  })
+                });
+
+              case 10:
+              case "end":
+                return _context.stop();
+            }
+          }
+        }, _callee, this);
+      }));
+
+      function configurePre() {
+        return _configurePre.apply(this, arguments);
+      }
+
+      return configurePre;
+    }()
+  }, {
     key: "configure",
     value: function () {
-      var _configure = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee() {
+      var _configure = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee2() {
         var _this = this;
 
-        var vcfGzLocation, location, indexType, filehandle, isCSI, vcf;
-        return runtime_1.wrap(function _callee$(_context) {
+        return runtime_1.wrap(function _callee2$(_context2) {
           while (1) {
-            switch (_context.prev = _context.next) {
+            switch (_context2.prev = _context2.next) {
               case 0:
                 if (!this.configured) {
-                  vcfGzLocation = readConfObject(this.config, 'vcfGzLocation');
-                  location = readConfObject(this.config, ['index', 'location']);
-                  indexType = readConfObject(this.config, ['index', 'indexType']);
-                  filehandle = openLocation(vcfGzLocation, this.pluginManager);
-                  isCSI = indexType === 'CSI';
-                  vcf = new TabixIndexedFile({
-                    filehandle: filehandle,
-                    csiFilehandle: isCSI ? openLocation(location, this.pluginManager) : undefined,
-                    tbiFilehandle: !isCSI ? openLocation(location, this.pluginManager) : undefined,
-                    chunkCacheSize: 50 * Math.pow(2, 20),
-                    chunkSizeLimit: 1000000000
-                  });
-                  this.configured = vcf.getHeader().then(function (header) {
-                    return {
-                      filehandle: filehandle,
-                      vcf: vcf,
-                      parser: new VCF({
-                        header: header
-                      })
-                    };
-                  })["catch"](function (e) {
+                  this.configured = this.configurePre()["catch"](function (e) {
                     _this.configured = undefined;
                     throw e;
                   });
                 }
 
-                return _context.abrupt("return", this.configured);
+                return _context2.abrupt("return", this.configured);
 
               case 2:
               case "end":
-                return _context.stop();
+                return _context2.stop();
             }
           }
-        }, _callee, this);
+        }, _callee2, this);
       }));
 
       function configure() {
@@ -1981,31 +2011,31 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getRefNames",
     value: function () {
-      var _getRefNames = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee2() {
+      var _getRefNames = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3() {
         var opts,
             _yield$this$configure,
             vcf,
-            _args2 = arguments;
+            _args3 = arguments;
 
-        return runtime_1.wrap(function _callee2$(_context2) {
+        return runtime_1.wrap(function _callee3$(_context3) {
           while (1) {
-            switch (_context2.prev = _context2.next) {
+            switch (_context3.prev = _context3.next) {
               case 0:
-                opts = _args2.length > 0 && _args2[0] !== undefined ? _args2[0] : {};
-                _context2.next = 3;
+                opts = _args3.length > 0 && _args3[0] !== undefined ? _args3[0] : {};
+                _context3.next = 3;
                 return this.configure();
 
               case 3:
-                _yield$this$configure = _context2.sent;
+                _yield$this$configure = _context3.sent;
                 vcf = _yield$this$configure.vcf;
-                return _context2.abrupt("return", vcf.getReferenceSequenceNames(opts));
+                return _context3.abrupt("return", vcf.getReferenceSequenceNames(opts));
 
               case 6:
               case "end":
-                return _context2.stop();
+                return _context3.stop();
             }
           }
-        }, _callee2, this);
+        }, _callee3, this);
       }));
 
       function getRefNames() {
@@ -2017,27 +2047,27 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getHeader",
     value: function () {
-      var _getHeader = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3() {
+      var _getHeader = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee4() {
         var _yield$this$configure2, vcf;
 
-        return runtime_1.wrap(function _callee3$(_context3) {
+        return runtime_1.wrap(function _callee4$(_context4) {
           while (1) {
-            switch (_context3.prev = _context3.next) {
+            switch (_context4.prev = _context4.next) {
               case 0:
-                _context3.next = 2;
+                _context4.next = 2;
                 return this.configure();
 
               case 2:
-                _yield$this$configure2 = _context3.sent;
+                _yield$this$configure2 = _context4.sent;
                 vcf = _yield$this$configure2.vcf;
-                return _context3.abrupt("return", vcf.getHeader());
+                return _context4.abrupt("return", vcf.getHeader());
 
               case 5:
               case "end":
-                return _context3.stop();
+                return _context4.stop();
             }
           }
-        }, _callee3, this);
+        }, _callee4, this);
       }));
 
       function getHeader() {
@@ -2049,27 +2079,27 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }, {
     key: "getMetadata",
     value: function () {
-      var _getMetadata = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee4() {
+      var _getMetadata = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee5() {
         var _yield$this$configure3, parser;
 
-        return runtime_1.wrap(function _callee4$(_context4) {
+        return runtime_1.wrap(function _callee5$(_context5) {
           while (1) {
-            switch (_context4.prev = _context4.next) {
+            switch (_context5.prev = _context5.next) {
               case 0:
-                _context4.next = 2;
+                _context5.next = 2;
                 return this.configure();
 
               case 2:
-                _yield$this$configure3 = _context4.sent;
+                _yield$this$configure3 = _context5.sent;
                 parser = _yield$this$configure3.parser;
-                return _context4.abrupt("return", parser.getMetadata());
+                return _context5.abrupt("return", parser.getMetadata());
 
               case 5:
               case "end":
-                return _context4.stop();
+                return _context5.stop();
             }
           }
-        }, _callee4, this);
+        }, _callee5, this);
       }));
 
       function getMetadata() {
@@ -2085,22 +2115,22 @@ var _default = /*#__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 _callee5(observer) {
+        var _ref = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee6(observer) {
           var refName, start, end, _yield$_this2$configu, vcf, parser;
 
-          return runtime_1.wrap(function _callee5$(_context5) {
+          return runtime_1.wrap(function _callee6$(_context6) {
             while (1) {
-              switch (_context5.prev = _context5.next) {
+              switch (_context6.prev = _context6.next) {
                 case 0:
                   refName = query.refName, start = query.start, end = query.end;
-                  _context5.next = 3;
+                  _context6.next = 3;
                   return _this2.configure();
 
                 case 3:
-                  _yield$_this2$configu = _context5.sent;
+                  _yield$_this2$configu = _context6.sent;
                   vcf = _yield$_this2$configu.vcf;
                   parser = _yield$_this2$configu.parser;
-                  _context5.next = 8;
+                  _context6.next = 8;
                   return vcf.getLines(refName, start, end, _objectSpread2({
                     lineCallback: function lineCallback(line, fileOffset) {
                       observer.next(new VCFFeature({
@@ -2116,10 +2146,10 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
                 case 9:
                 case "end":
-                  return _context5.stop();
+                  return _context6.stop();
               }
             }
-          }, _callee5);
+          }, _callee6);
         }));
 
         return function (_x) {
@@ -2154,29 +2184,35 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
       var superGetFeaturesInMultipleRegions = _get(_getPrototypeOf(_default.prototype), "getFeaturesInMultipleRegions", this);
 
       return ObservableCreate( /*#__PURE__*/function () {
-        var _ref2 = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee6(observer) {
-          var bytes, _yield$_this3$configu, filehandle, stat, pct;
+        var _ref2 = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee7(observer) {
+          var _yield$_this3$configu, vcf, bytes, _yield$_this3$configu2, filehandle, stat, pct;
 
-          return runtime_1.wrap(function _callee6$(_context6) {
+          return runtime_1.wrap(function _callee7$(_context7) {
             while (1) {
-              switch (_context6.prev = _context6.next) {
+              switch (_context7.prev = _context7.next) {
                 case 0:
-                  _context6.next = 2;
-                  return _this3.bytesForRegions(regions);
+                  _context7.next = 2;
+                  return _this3.configure();
 
                 case 2:
-                  bytes = _context6.sent;
-                  _context6.next = 5;
+                  _yield$_this3$configu = _context7.sent;
+                  vcf = _yield$_this3$configu.vcf;
+                  _context7.next = 6;
+                  return bytesForRegions(regions, vcf.index);
+
+                case 6:
+                  bytes = _context7.sent;
+                  _context7.next = 9;
                   return _this3.configure();
 
-                case 5:
-                  _yield$_this3$configu = _context6.sent;
-                  filehandle = _yield$_this3$configu.filehandle;
-                  _context6.next = 9;
+                case 9:
+                  _yield$_this3$configu2 = _context7.sent;
+                  filehandle = _yield$_this3$configu2.filehandle;
+                  _context7.next = 13;
                   return filehandle.stat();
 
-                case 9:
-                  stat = _context6.sent;
+                case 13:
+                  stat = _context7.sent;
                   pct = Math.round(bytes / stat.size * 100);
 
                   if (pct > 100) {
@@ -2190,12 +2226,12 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
                   superGetFeaturesInMultipleRegions.call(_this3, regions, opts).subscribe(observer); // super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)
 
-                case 14:
+                case 18:
                 case "end":
-                  return _context6.stop();
+                  return _context7.stop();
               }
             }
-          }, _callee6);
+          }, _callee7);
         }));
 
         return function (_x2) {
@@ -2203,77 +2239,6 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
         };
       }());
     }
-    /**
-     * get the approximate number of bytes queried from the file for the given
-     * query regions
-     * @param regions - list of query regions
-     */
-
-  }, {
-    key: "bytesForRegions",
-    value: function () {
-      var _bytesForRegions = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee7(regions) {
-        var _yield$this$configure4, vcf, blockResults, byteRanges;
-
-        return runtime_1.wrap(function _callee7$(_context7) {
-          while (1) {
-            switch (_context7.prev = _context7.next) {
-              case 0:
-                _context7.next = 2;
-                return this.configure();
-
-              case 2:
-                _yield$this$configure4 = _context7.sent;
-                vcf = _yield$this$configure4.vcf;
-                _context7.next = 6;
-                return Promise.all(regions.map(function (region) {
-                  return (// @ts-ignore
-                    vcf.index.blocksForRange(region.refName, region.start, region.end)
-                  );
-                }));
-
-              case 6:
-                blockResults = _context7.sent;
-                byteRanges = [];
-                blockResults.forEach(function (blocks) {
-                  blocks.forEach(function (block) {
-                    var start = block.minv.blockPosition;
-                    var end = block.maxv.blockPosition + 64000;
-
-                    if (!byteRanges.find(function (range) {
-                      if (range.start <= end && range.end >= start) {
-                        range.start = Math.min(range.start, start);
-                        range.end = Math.max(range.end, end);
-                        return true;
-                      }
-
-                      return false;
-                    })) {
-                      byteRanges.push({
-                        start: start,
-                        end: end
-                      });
-                    }
-                  });
-                });
-                return _context7.abrupt("return", byteRanges.reduce(function (a, b) {
-                  return a + b.end - b.start + 1;
-                }, 0));
-
-              case 10:
-              case "end":
-                return _context7.stop();
-            }
-          }
-        }, _callee7, this);
-      }));
-
-      function bytesForRegions(_x3) {
-        return _bytesForRegions.apply(this, arguments);
-      }
-
-      return bytesForRegions;
-    }()
   }, {
     key: "freeResources",
     value: function