@jbrowse/plugin-variants 1.5.6 → 1.6.0

package/dist/LinearVariantDisplay/model.d.ts

@@ -54,6 +54,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearBasicDisplay">;
     trackShowLabels: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
@@ -117,15 +118,17 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
+    currBpPerPx: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: Feature | undefined;
     scrollTop: number;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
     readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
-    readonly maxViewBpPerPx: any;
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
@@ -136,14 +139,28 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     getFeatureOverlapping(blockKey: string, x: number, y: number): any;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly estimatedStatsReady: boolean;
+    readonly maxAllowableBytes: number;
 } & {
+    setMessage(message: string): void;
     afterAttach(): void;
+    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
+        headers?: Record<string, string> | undefined;
+        signal?: AbortSignal | undefined;
+        filters?: string[] | undefined;
+    }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
+    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    setUserBpPerPxLimit(limit: number): void;
-    setMessage(message: string): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: Feature): void;
     clearFeatureSelection(): void;
@@ -151,7 +168,13 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     reload(): void;
     setContextMenuFeature(feature?: Feature | undefined): void;
 } & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
@@ -161,7 +184,7 @@ export default function (configSchema: LinearVariantDisplayConfigModel): import(
     }[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
     }): Promise<JSX.Element>;
 } & {

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -2,18 +2,15 @@ import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters
 import { NoAssemblyRegion, Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { TabixIndexedFile } from '@gmod/tabix';
-import { GenericFilehandle } from 'generic-filehandle';
 import VcfParser from '@gmod/vcf';
+import { GenericFilehandle } from 'generic-filehandle';
 export default class extends BaseFeatureDataAdapter {
-    protected configured?: Promise<{
-        vcf: TabixIndexedFile;
-        parser: VcfParser;
-        filehandle: GenericFilehandle;
-    }>;
+    private configured?;
+    private configurePre;
     protected configure(): Promise<{
+        filehandle: GenericFilehandle;
         vcf: TabixIndexedFile;
         parser: VcfParser;
-        filehandle: GenericFilehandle;
     }>;
     getRefNames(opts?: BaseOptions): Promise<any>;
     getHeader(): Promise<string>;
@@ -34,11 +31,5 @@ export default class extends BaseFeatureDataAdapter {
      * @returns Observable of Feature objects in the regions
      */
     getFeaturesInMultipleRegions(regions: Region[], opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    /**
-     * get the approximate number of bytes queried from the file for the given
-     * query regions
-     * @param regions - list of query regions
-     */
-    private bytesForRegions;
     freeResources(): void;
 }

package/dist/plugin-variants.cjs.development.js

@@ -144,14 +144,14 @@ 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);
@@ -1826,16 +1826,19 @@ var VariantsPlugin = /*#__PURE__*/function (_Plugin) {
           var adapterName = 'VcfTabixAdapter';
           var fileName = tracks.getFileName(file);
           var indexName = index && tracks.getFileName(index);
+          var obj = {
+            type: adapterName,
+            vcfGzLocation: file,
+            index: {
+              location: index || tracks.makeIndex(file, '.tbi'),
+              indexType: tracks.makeIndexType(indexName, 'CSI', 'TBI')
+            }
+          };
 
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              vcfGzLocation: file,
-              index: {
-                location: index || tracks.makeIndex(file, '.tbi'),
-                indexType: tracks.makeIndexType(indexName, 'CSI', 'TBI')
-              }
-            };
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
           }
 
           return adapterGuesser(file, index, adapterHint);
@@ -1933,51 +1936,78 @@ 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 = configuration.readConfObject(this.config, 'vcfGzLocation');
+                location = configuration.readConfObject(this.config, ['index', 'location']);
+                indexType = configuration.readConfObject(this.config, ['index', 'indexType']);
+                filehandle = io.openLocation(vcfGzLocation, this.pluginManager);
+                isCSI = indexType === 'CSI';
+                vcf = new tabix.TabixIndexedFile({
+                  filehandle: filehandle,
+                  csiFilehandle: isCSI ? io.openLocation(location, this.pluginManager) : undefined,
+                  tbiFilehandle: !isCSI ? 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();
+            }
+          }
+        }, _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 = configuration.readConfObject(this.config, 'vcfGzLocation');
-                  location = configuration.readConfObject(this.config, ['index', 'location']);
-                  indexType = configuration.readConfObject(this.config, ['index', 'indexType']);
-                  filehandle = io.openLocation(vcfGzLocation, this.pluginManager);
-                  isCSI = indexType === 'CSI';
-                  vcf = new tabix.TabixIndexedFile({
-                    filehandle: filehandle,
-                    csiFilehandle: isCSI ? io.openLocation(location, this.pluginManager) : undefined,
-                    tbiFilehandle: !isCSI ? io.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__default({
-                        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() {
@@ -1989,31 +2019,31 @@ 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() {
@@ -2025,27 +2055,27 @@ 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() {
@@ -2057,27 +2087,27 @@ 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() {
@@ -2093,22 +2123,22 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
       var opts = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {};
       return rxjs.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({
@@ -2124,10 +2154,10 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
                 case 9:
                 case "end":
-                  return _context5.stop();
+                  return _context6.stop();
               }
             }
-          }, _callee5);
+          }, _callee6);
         }));
 
         return function (_x) {
@@ -2162,29 +2192,35 @@ var _default = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
       var superGetFeaturesInMultipleRegions = _get(_getPrototypeOf(_default.prototype), "getFeaturesInMultipleRegions", this);
 
       return rxjs.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 util.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) {
@@ -2198,12 +2234,12 @@ 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) {
@@ -2211,77 +2247,6 @@ 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