@jbrowse/plugin-bed 1.4.3 → 1.5.2

package/dist/BedTabixAdapter/BedTabixAdapter.d.ts

@@ -4,13 +4,15 @@ import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { TabixIndexedFile } from '@gmod/tabix';
 import { Instance } from 'mobx-state-tree';
 import MyConfigSchema from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     private parser;
     protected bed: TabixIndexedFile;
     protected columnNames: string[];
     protected scoreColumn: string;
     static capabilities: string[];
-    constructor(config: Instance<typeof MyConfigSchema>);
+    constructor(config: Instance<typeof MyConfigSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(opts?: BaseOptions): Promise<any>;
     getHeader(): Promise<string>;
     defaultParser(fields: string[], line: string): {

package/dist/BigBedAdapter/BigBedAdapter.d.ts

@@ -3,10 +3,12 @@ import { Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { Instance } from 'mobx-state-tree';
 import configSchema from './configSchema';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
 export default class BigBedAdapter extends BaseFeatureDataAdapter {
     private bigbed;
     private parser;
-    constructor(config: Instance<typeof configSchema>);
+    constructor(config: Instance<typeof configSchema>, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
     getRefNames(): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<{
         version: any;

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

@@ -8,6 +8,7 @@ var AdapterType = _interopDefault(require('@jbrowse/core/pluggableElementTypes/A
 var Plugin = _interopDefault(require('@jbrowse/core/Plugin'));
 var configuration = require('@jbrowse/core/configuration');
 var mobxStateTree = require('mobx-state-tree');
+var tracks = require('@jbrowse/core/util/tracks');
 var bbi = require('@gmod/bbi');
 var BED = _interopDefault(require('@gmod/bed'));
 var BaseAdapter = require('@jbrowse/core/data_adapters/BaseAdapter');
@@ -219,6 +220,8 @@ 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);
@@ -247,7 +250,8 @@ var bigBedAdapterConfigSchema = /*#__PURE__*/configuration.ConfigurationSchema('
   bigBedLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/my.bb'
+      uri: '/path/to/my.bb',
+      locationType: 'UriLocation'
     }
   }
 }, {
@@ -258,7 +262,8 @@ var bedTabixAdapterConfigSchema = /*#__PURE__*/configuration.ConfigurationSchema
   bedGzLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/my.bed.gz'
+      uri: '/path/to/my.bed.gz',
+      locationType: 'UriLocation'
     }
   },
   index: /*#__PURE__*/configuration.ConfigurationSchema('TabixIndex', {
@@ -270,7 +275,8 @@ var bedTabixAdapterConfigSchema = /*#__PURE__*/configuration.ConfigurationSchema
     location: {
       type: 'fileLocation',
       defaultValue: {
-        uri: '/path/to/my.bed.gz.tbi'
+        uri: '/path/to/my.bed.gz.tbi',
+        locationType: 'UriLocation'
       }
     }
   }),
@@ -322,6 +328,22 @@ var BedPlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(bb|bigbed)$/i;
+          var adapterName = 'BigBedAdapter';
+          var fileName = tracks.getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bigBedLocation: file
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'BedTabixAdapter',
@@ -333,6 +355,27 @@ var BedPlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.bed\.b?gz$/i;
+          var adapterName = 'BedTabixAdapter';
+          var fileName = tracks.getFileName(file);
+          var indexName = index && tracks.getFileName(index);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bedGzLocation: file,
+              index: {
+                location: index || tracks.makeIndex(file, '.tbi'),
+                indexType: tracks.makeIndexType(indexName, 'CSI', 'TBI')
+              }
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
     }
   }]);
 
@@ -436,11 +479,9 @@ 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([])));
 
@@ -451,8 +492,9 @@ 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.
 
@@ -557,11 +599,9 @@ 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.
@@ -738,13 +778,12 @@ 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 = {
@@ -1056,14 +1095,19 @@ 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);
+    }
   }
 });
 
@@ -1181,22 +1225,23 @@ function ucscProcessedTranscript(feature) {
   return newFeature;
 }
 
-var _excluded = ["fields"];
+var _excluded = ["fields"],
+    _excluded2 = ["chromStart", "chromEnd", "chrom"];
 
 var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   _inherits(BigBedAdapter, _BaseFeatureDataAdapt);
 
   var _super = /*#__PURE__*/_createSuper(BigBedAdapter);
 
-  function BigBedAdapter(config) {
+  function BigBedAdapter(config, getSubAdapter, pluginManager) {
     var _this;
 
     _classCallCheck(this, BigBedAdapter);
 
-    _this = _super.call(this, config);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
     var bigBedLocation = configuration.readConfObject(config, 'bigBedLocation');
     _this.bigbed = new bbi.BigBed({
-      filehandle: io.openLocation(bigBedLocation)
+      filehandle: io.openLocation(bigBedLocation, _this.pluginManager)
     });
     _this.parser = _this.bigbed.getHeader().then(function (_ref) {
       var autoSql = _ref.autoSql;
@@ -1389,12 +1434,11 @@ var BigBedAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                       throw new Error('invalid bbi feature');
                     }
 
-                    delete data.chromStart;
-                    delete data.chromEnd;
-                    delete data.chrom;
+                    var rest = _objectWithoutProperties(data, _excluded2);
+
                     var f = new SimpleFeature({
                       id: "".concat(_this2.id, "-").concat(r.uniqueId),
-                      data: _objectSpread2(_objectSpread2({}, data), {}, {
+                      data: _objectSpread2(_objectSpread2({}, rest), {}, {
                         start: r.start,
                         end: r.end,
                         refName: refName
@@ -1444,21 +1488,21 @@ var BedTabixAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
 
   var _super = /*#__PURE__*/_createSuper(BedTabixAdapter);
 
-  function BedTabixAdapter(config) {
+  function BedTabixAdapter(config, getSubAdapter, pluginManager) {
     var _this;
 
     _classCallCheck(this, BedTabixAdapter);
 
-    _this = _super.call(this, config);
+    _this = _super.call(this, config, getSubAdapter, pluginManager);
     var bedGzLocation = configuration.readConfObject(config, 'bedGzLocation');
     var index = configuration.readConfObject(config, 'index');
     var autoSql = configuration.readConfObject(config, 'autoSql');
     var location = index.location,
         indexType = index.indexType;
     _this.bed = new tabix.TabixIndexedFile({
-      filehandle: io.openLocation(bedGzLocation),
-      csiFilehandle: indexType === 'CSI' ? io.openLocation(location) : undefined,
-      tbiFilehandle: indexType !== 'CSI' ? io.openLocation(location) : undefined,
+      filehandle: io.openLocation(bedGzLocation, _this.pluginManager),
+      csiFilehandle: indexType === 'CSI' ? io.openLocation(location, _this.pluginManager) : undefined,
+      tbiFilehandle: indexType !== 'CSI' ? io.openLocation(location, _this.pluginManager) : undefined,
       chunkCacheSize: 50 * Math.pow(2, 20)
     });
     _this.columnNames = configuration.readConfObject(config, 'columnNames');