@jbrowse/plugin-bed 1.4.3 → 1.5.2

package/dist/plugin-bed.cjs.production.min.js.map

@@ -1 +1 @@
-{"version":3,"file":"plugin-bed.cjs.production.min.js","sources":["../src/BigBedAdapter/configSchema.ts","../src/BedTabixAdapter/configSchema.ts","../src/index.ts","../../../node_modules/regenerator-runtime/runtime.js","../src/util.ts","../src/BigBedAdapter/BigBedAdapter.ts","../src/BedTabixAdapter/BedTabixAdapter.ts"],"sourcesContent":["import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'BigBedAdapter',\n  {\n    bigBedLocation: {\n      type: 'fileLocation',\n      defaultValue: { uri: '/path/to/my.bb' },\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default ConfigurationSchema(\n  'BedTabixAdapter',\n  {\n    bedGzLocation: {\n      type: 'fileLocation',\n      defaultValue: { uri: '/path/to/my.bed.gz' },\n    },\n\n    index: ConfigurationSchema('TabixIndex', {\n      indexType: {\n        model: types.enumeration('IndexType', ['TBI', 'CSI']),\n        type: 'stringEnum',\n        defaultValue: 'TBI',\n      },\n      location: {\n        type: 'fileLocation',\n        defaultValue: { uri: '/path/to/my.bed.gz.tbi' },\n      },\n    }),\n\n    columnNames: {\n      type: 'stringArray',\n      description: 'List of column names',\n      defaultValue: [],\n    },\n\n    scoreColumn: {\n      type: 'string',\n      description: 'The column to use as a \"score\" attribute',\n      defaultValue: '',\n    },\n\n    autoSql: {\n      type: 'string',\n      description: 'The autoSql definition for the data fields in the file',\n      defaultValue: '',\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { configSchema as bigBedAdapterConfigSchema } from './BigBedAdapter'\nimport { configSchema as bedTabixAdapterConfigSchema } from './BedTabixAdapter'\n\nexport default class BedPlugin extends Plugin {\n  name = 'BedPlugin'\n\n  install(pluginManager: PluginManager) {\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'BigBedAdapter',\n          configSchema: bigBedAdapterConfigSchema,\n          getAdapterClass: () =>\n            import('./BigBedAdapter/BigBedAdapter').then(r => r.default),\n        }),\n    )\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'BedTabixAdapter',\n          configSchema: bedTabixAdapterConfigSchema,\n          getAdapterClass: () =>\n            import('./BedTabixAdapter/BedTabixAdapter').then(r => r.default),\n        }),\n    )\n  }\n}\n","/**\n * Copyright (c) 2014-present, Facebook, Inc.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\nvar runtime = (function (exports) {\n  \"use strict\";\n\n  var Op = Object.prototype;\n  var hasOwn = Op.hasOwnProperty;\n  var undefined; // More compressible than void 0.\n  var $Symbol = typeof Symbol === \"function\" ? Symbol : {};\n  var iteratorSymbol = $Symbol.iterator || \"@@iterator\";\n  var asyncIteratorSymbol = $Symbol.asyncIterator || \"@@asyncIterator\";\n  var toStringTagSymbol = $Symbol.toStringTag || \"@@toStringTag\";\n\n  function define(obj, key, value) {\n    Object.defineProperty(obj, key, {\n      value: value,\n      enumerable: true,\n      configurable: true,\n      writable: true\n    });\n    return obj[key];\n  }\n  try {\n    // IE 8 has a broken Object.defineProperty that only works on DOM objects.\n    define({}, \"\");\n  } catch (err) {\n    define = function(obj, key, value) {\n      return obj[key] = value;\n    };\n  }\n\n  function wrap(innerFn, outerFn, self, tryLocsList) {\n    // If outerFn provided and outerFn.prototype is a Generator, then outerFn.prototype instanceof Generator.\n    var protoGenerator = outerFn && outerFn.prototype instanceof Generator ? outerFn : Generator;\n    var generator = Object.create(protoGenerator.prototype);\n    var context = new Context(tryLocsList || []);\n\n    // The ._invoke method unifies the implementations of the .next,\n    // .throw, and .return methods.\n    generator._invoke = makeInvokeMethod(innerFn, self, context);\n\n    return generator;\n  }\n  exports.wrap = wrap;\n\n  // Try/catch helper to minimize deoptimizations. Returns a completion\n  // record like context.tryEntries[i].completion. This interface could\n  // have been (and was previously) designed to take a closure to be\n  // invoked without arguments, but in all the cases we care about we\n  // already have an existing method we want to call, so there's no need\n  // to create a new function object. We can even get away with assuming\n  // the method takes exactly one argument, since that happens to be true\n  // in every case, so we don't have to touch the arguments object. The\n  // only additional allocation required is the completion record, which\n  // has a stable shape and so hopefully should be cheap to allocate.\n  function tryCatch(fn, obj, arg) {\n    try {\n      return { type: \"normal\", arg: fn.call(obj, arg) };\n    } catch (err) {\n      return { type: \"throw\", arg: err };\n    }\n  }\n\n  var GenStateSuspendedStart = \"suspendedStart\";\n  var GenStateSuspendedYield = \"suspendedYield\";\n  var GenStateExecuting = \"executing\";\n  var GenStateCompleted = \"completed\";\n\n  // Returning this object from the innerFn has the same effect as\n  // breaking out of the dispatch switch statement.\n  var ContinueSentinel = {};\n\n  // Dummy constructor functions that we use as the .constructor and\n  // .constructor.prototype properties for functions that return Generator\n  // objects. For full spec compliance, you may wish to configure your\n  // minifier not to mangle the names of these two functions.\n  function Generator() {}\n  function GeneratorFunction() {}\n  function GeneratorFunctionPrototype() {}\n\n  // This is a polyfill for %IteratorPrototype% for environments that\n  // don't natively support it.\n  var IteratorPrototype = {};\n  IteratorPrototype[iteratorSymbol] = function () {\n    return this;\n  };\n\n  var getProto = Object.getPrototypeOf;\n  var NativeIteratorPrototype = getProto && getProto(getProto(values([])));\n  if (NativeIteratorPrototype &&\n      NativeIteratorPrototype !== Op &&\n      hasOwn.call(NativeIteratorPrototype, iteratorSymbol)) {\n    // This environment has a native %IteratorPrototype%; use it instead\n    // of the polyfill.\n    IteratorPrototype = NativeIteratorPrototype;\n  }\n\n  var Gp = GeneratorFunctionPrototype.prototype =\n    Generator.prototype = Object.create(IteratorPrototype);\n  GeneratorFunction.prototype = Gp.constructor = GeneratorFunctionPrototype;\n  GeneratorFunctionPrototype.constructor = GeneratorFunction;\n  GeneratorFunction.displayName = define(\n    GeneratorFunctionPrototype,\n    toStringTagSymbol,\n    \"GeneratorFunction\"\n  );\n\n  // Helper for defining the .next, .throw, and .return methods of the\n  // Iterator interface in terms of a single ._invoke method.\n  function defineIteratorMethods(prototype) {\n    [\"next\", \"throw\", \"return\"].forEach(function(method) {\n      define(prototype, method, function(arg) {\n        return this._invoke(method, arg);\n      });\n    });\n  }\n\n  exports.isGeneratorFunction = function(genFun) {\n    var ctor = typeof genFun === \"function\" && genFun.constructor;\n    return ctor\n      ? ctor === GeneratorFunction ||\n        // For the native GeneratorFunction constructor, the best we can\n        // do is to check its .name property.\n        (ctor.displayName || ctor.name) === \"GeneratorFunction\"\n      : false;\n  };\n\n  exports.mark = function(genFun) {\n    if (Object.setPrototypeOf) {\n      Object.setPrototypeOf(genFun, GeneratorFunctionPrototype);\n    } else {\n      genFun.__proto__ = GeneratorFunctionPrototype;\n      define(genFun, toStringTagSymbol, \"GeneratorFunction\");\n    }\n    genFun.prototype = Object.create(Gp);\n    return genFun;\n  };\n\n  // Within the body of any async function, `await x` is transformed to\n  // `yield regeneratorRuntime.awrap(x)`, so that the runtime can test\n  // `hasOwn.call(value, \"__await\")` to determine if the yielded value is\n  // meant to be awaited.\n  exports.awrap = function(arg) {\n    return { __await: arg };\n  };\n\n  function AsyncIterator(generator, PromiseImpl) {\n    function invoke(method, arg, resolve, reject) {\n      var record = tryCatch(generator[method], generator, arg);\n      if (record.type === \"throw\") {\n        reject(record.arg);\n      } else {\n        var result = record.arg;\n        var value = result.value;\n        if (value &&\n            typeof value === \"object\" &&\n            hasOwn.call(value, \"__await\")) {\n          return PromiseImpl.resolve(value.__await).then(function(value) {\n            invoke(\"next\", value, resolve, reject);\n          }, function(err) {\n            invoke(\"throw\", err, resolve, reject);\n          });\n        }\n\n        return PromiseImpl.resolve(value).then(function(unwrapped) {\n          // When a yielded Promise is resolved, its final value becomes\n          // the .value of the Promise<{value,done}> result for the\n          // current iteration.\n          result.value = unwrapped;\n          resolve(result);\n        }, function(error) {\n          // If a rejected Promise was yielded, throw the rejection back\n          // into the async generator function so it can be handled there.\n          return invoke(\"throw\", error, resolve, reject);\n        });\n      }\n    }\n\n    var previousPromise;\n\n    function enqueue(method, arg) {\n      function callInvokeWithMethodAndArg() {\n        return new PromiseImpl(function(resolve, reject) {\n          invoke(method, arg, resolve, reject);\n        });\n      }\n\n      return previousPromise =\n        // If enqueue has been called before, then we want to wait until\n        // all previous Promises have been resolved before calling invoke,\n        // so that results are always delivered in the correct order. If\n        // enqueue has not been called before, then it is important to\n        // call invoke immediately, without waiting on a callback to fire,\n        // so that the async generator function has the opportunity to do\n        // any necessary setup in a predictable way. This predictability\n        // is why the Promise constructor synchronously invokes its\n        // executor callback, and why async functions synchronously\n        // execute code before the first await. Since we implement simple\n        // async functions in terms of async generators, it is especially\n        // important to get this right, even though it requires care.\n        previousPromise ? previousPromise.then(\n          callInvokeWithMethodAndArg,\n          // Avoid propagating failures to Promises returned by later\n          // invocations of the iterator.\n          callInvokeWithMethodAndArg\n        ) : callInvokeWithMethodAndArg();\n    }\n\n    // Define the unified helper method that is used to implement .next,\n    // .throw, and .return (see defineIteratorMethods).\n    this._invoke = enqueue;\n  }\n\n  defineIteratorMethods(AsyncIterator.prototype);\n  AsyncIterator.prototype[asyncIteratorSymbol] = function () {\n    return this;\n  };\n  exports.AsyncIterator = AsyncIterator;\n\n  // Note that simple async functions are implemented on top of\n  // AsyncIterator objects; they just return a Promise for the value of\n  // the final result produced by the iterator.\n  exports.async = function(innerFn, outerFn, self, tryLocsList, PromiseImpl) {\n    if (PromiseImpl === void 0) PromiseImpl = Promise;\n\n    var iter = new AsyncIterator(\n      wrap(innerFn, outerFn, self, tryLocsList),\n      PromiseImpl\n    );\n\n    return exports.isGeneratorFunction(outerFn)\n      ? iter // If outerFn is a generator, return the full iterator.\n      : iter.next().then(function(result) {\n          return result.done ? result.value : iter.next();\n        });\n  };\n\n  function makeInvokeMethod(innerFn, self, context) {\n    var state = GenStateSuspendedStart;\n\n    return function invoke(method, arg) {\n      if (state === GenStateExecuting) {\n        throw new Error(\"Generator is already running\");\n      }\n\n      if (state === GenStateCompleted) {\n        if (method === \"throw\") {\n          throw arg;\n        }\n\n        // Be forgiving, per 25.3.3.3.3 of the spec:\n        // https://people.mozilla.org/~jorendorff/es6-draft.html#sec-generatorresume\n        return doneResult();\n      }\n\n      context.method = method;\n      context.arg = arg;\n\n      while (true) {\n        var delegate = context.delegate;\n        if (delegate) {\n          var delegateResult = maybeInvokeDelegate(delegate, context);\n          if (delegateResult) {\n            if (delegateResult === ContinueSentinel) continue;\n            return delegateResult;\n          }\n        }\n\n        if (context.method === \"next\") {\n          // Setting context._sent for legacy support of Babel's\n          // function.sent implementation.\n          context.sent = context._sent = context.arg;\n\n        } else if (context.method === \"throw\") {\n          if (state === GenStateSuspendedStart) {\n            state = GenStateCompleted;\n            throw context.arg;\n          }\n\n          context.dispatchException(context.arg);\n\n        } else if (context.method === \"return\") {\n          context.abrupt(\"return\", context.arg);\n        }\n\n        state = GenStateExecuting;\n\n        var record = tryCatch(innerFn, self, context);\n        if (record.type === \"normal\") {\n          // If an exception is thrown from innerFn, we leave state ===\n          // GenStateExecuting and loop back for another invocation.\n          state = context.done\n            ? GenStateCompleted\n            : GenStateSuspendedYield;\n\n          if (record.arg === ContinueSentinel) {\n            continue;\n          }\n\n          return {\n            value: record.arg,\n            done: context.done\n          };\n\n        } else if (record.type === \"throw\") {\n          state = GenStateCompleted;\n          // Dispatch the exception by looping back around to the\n          // context.dispatchException(context.arg) call above.\n          context.method = \"throw\";\n          context.arg = record.arg;\n        }\n      }\n    };\n  }\n\n  // Call delegate.iterator[context.method](context.arg) and handle the\n  // result, either by returning a { value, done } result from the\n  // delegate iterator, or by modifying context.method and context.arg,\n  // setting context.delegate to null, and returning the ContinueSentinel.\n  function maybeInvokeDelegate(delegate, context) {\n    var method = delegate.iterator[context.method];\n    if (method === undefined) {\n      // A .throw or .return when the delegate iterator has no .throw\n      // method always terminates the yield* loop.\n      context.delegate = null;\n\n      if (context.method === \"throw\") {\n        // Note: [\"return\"] must be used for ES3 parsing compatibility.\n        if (delegate.iterator[\"return\"]) {\n          // If the delegate iterator has a return method, give it a\n          // chance to clean up.\n          context.method = \"return\";\n          context.arg = undefined;\n          maybeInvokeDelegate(delegate, context);\n\n          if (context.method === \"throw\") {\n            // If maybeInvokeDelegate(context) changed context.method from\n            // \"return\" to \"throw\", let that override the TypeError below.\n            return ContinueSentinel;\n          }\n        }\n\n        context.method = \"throw\";\n        context.arg = new TypeError(\n          \"The iterator does not provide a 'throw' method\");\n      }\n\n      return ContinueSentinel;\n    }\n\n    var record = tryCatch(method, delegate.iterator, context.arg);\n\n    if (record.type === \"throw\") {\n      context.method = \"throw\";\n      context.arg = record.arg;\n      context.delegate = null;\n      return ContinueSentinel;\n    }\n\n    var info = record.arg;\n\n    if (! info) {\n      context.method = \"throw\";\n      context.arg = new TypeError(\"iterator result is not an object\");\n      context.delegate = null;\n      return ContinueSentinel;\n    }\n\n    if (info.done) {\n      // Assign the result of the finished delegate to the temporary\n      // variable specified by delegate.resultName (see delegateYield).\n      context[delegate.resultName] = info.value;\n\n      // Resume execution at the desired location (see delegateYield).\n      context.next = delegate.nextLoc;\n\n      // If context.method was \"throw\" but the delegate handled the\n      // exception, let the outer generator proceed normally. If\n      // context.method was \"next\", forget context.arg since it has been\n      // \"consumed\" by the delegate iterator. If context.method was\n      // \"return\", allow the original .return call to continue in the\n      // outer generator.\n      if (context.method !== \"return\") {\n        context.method = \"next\";\n        context.arg = undefined;\n      }\n\n    } else {\n      // Re-yield the result returned by the delegate method.\n      return info;\n    }\n\n    // The delegate iterator is finished, so forget it and continue with\n    // the outer generator.\n    context.delegate = null;\n    return ContinueSentinel;\n  }\n\n  // Define Generator.prototype.{next,throw,return} in terms of the\n  // unified ._invoke helper method.\n  defineIteratorMethods(Gp);\n\n  define(Gp, toStringTagSymbol, \"Generator\");\n\n  // A Generator should always return itself as the iterator object when the\n  // @@iterator function is called on it. Some browsers' implementations of the\n  // iterator prototype chain incorrectly implement this, causing the Generator\n  // object to not be returned from this call. This ensures that doesn't happen.\n  // See https://github.com/facebook/regenerator/issues/274 for more details.\n  Gp[iteratorSymbol] = function() {\n    return this;\n  };\n\n  Gp.toString = function() {\n    return \"[object Generator]\";\n  };\n\n  function pushTryEntry(locs) {\n    var entry = { tryLoc: locs[0] };\n\n    if (1 in locs) {\n      entry.catchLoc = locs[1];\n    }\n\n    if (2 in locs) {\n      entry.finallyLoc = locs[2];\n      entry.afterLoc = locs[3];\n    }\n\n    this.tryEntries.push(entry);\n  }\n\n  function resetTryEntry(entry) {\n    var record = entry.completion || {};\n    record.type = \"normal\";\n    delete record.arg;\n    entry.completion = record;\n  }\n\n  function Context(tryLocsList) {\n    // The root entry object (effectively a try statement without a catch\n    // or a finally block) gives us a place to store values thrown from\n    // locations where there is no enclosing try statement.\n    this.tryEntries = [{ tryLoc: \"root\" }];\n    tryLocsList.forEach(pushTryEntry, this);\n    this.reset(true);\n  }\n\n  exports.keys = function(object) {\n    var keys = [];\n    for (var key in object) {\n      keys.push(key);\n    }\n    keys.reverse();\n\n    // Rather than returning an object with a next method, we keep\n    // things simple and return the next function itself.\n    return function next() {\n      while (keys.length) {\n        var key = keys.pop();\n        if (key in object) {\n          next.value = key;\n          next.done = false;\n          return next;\n        }\n      }\n\n      // To avoid creating an additional object, we just hang the .value\n      // and .done properties off the next function object itself. This\n      // also ensures that the minifier will not anonymize the function.\n      next.done = true;\n      return next;\n    };\n  };\n\n  function values(iterable) {\n    if (iterable) {\n      var iteratorMethod = iterable[iteratorSymbol];\n      if (iteratorMethod) {\n        return iteratorMethod.call(iterable);\n      }\n\n      if (typeof iterable.next === \"function\") {\n        return iterable;\n      }\n\n      if (!isNaN(iterable.length)) {\n        var i = -1, next = function next() {\n          while (++i < iterable.length) {\n            if (hasOwn.call(iterable, i)) {\n              next.value = iterable[i];\n              next.done = false;\n              return next;\n            }\n          }\n\n          next.value = undefined;\n          next.done = true;\n\n          return next;\n        };\n\n        return next.next = next;\n      }\n    }\n\n    // Return an iterator with no values.\n    return { next: doneResult };\n  }\n  exports.values = values;\n\n  function doneResult() {\n    return { value: undefined, done: true };\n  }\n\n  Context.prototype = {\n    constructor: Context,\n\n    reset: function(skipTempReset) {\n      this.prev = 0;\n      this.next = 0;\n      // Resetting context._sent for legacy support of Babel's\n      // function.sent implementation.\n      this.sent = this._sent = undefined;\n      this.done = false;\n      this.delegate = null;\n\n      this.method = \"next\";\n      this.arg = undefined;\n\n      this.tryEntries.forEach(resetTryEntry);\n\n      if (!skipTempReset) {\n        for (var name in this) {\n          // Not sure about the optimal order of these conditions:\n          if (name.charAt(0) === \"t\" &&\n              hasOwn.call(this, name) &&\n              !isNaN(+name.slice(1))) {\n            this[name] = undefined;\n          }\n        }\n      }\n    },\n\n    stop: function() {\n      this.done = true;\n\n      var rootEntry = this.tryEntries[0];\n      var rootRecord = rootEntry.completion;\n      if (rootRecord.type === \"throw\") {\n        throw rootRecord.arg;\n      }\n\n      return this.rval;\n    },\n\n    dispatchException: function(exception) {\n      if (this.done) {\n        throw exception;\n      }\n\n      var context = this;\n      function handle(loc, caught) {\n        record.type = \"throw\";\n        record.arg = exception;\n        context.next = loc;\n\n        if (caught) {\n          // If the dispatched exception was caught by a catch block,\n          // then let that catch block handle the exception normally.\n          context.method = \"next\";\n          context.arg = undefined;\n        }\n\n        return !! caught;\n      }\n\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        var record = entry.completion;\n\n        if (entry.tryLoc === \"root\") {\n          // Exception thrown outside of any try block that could handle\n          // it, so set the completion value of the entire function to\n          // throw the exception.\n          return handle(\"end\");\n        }\n\n        if (entry.tryLoc <= this.prev) {\n          var hasCatch = hasOwn.call(entry, \"catchLoc\");\n          var hasFinally = hasOwn.call(entry, \"finallyLoc\");\n\n          if (hasCatch && hasFinally) {\n            if (this.prev < entry.catchLoc) {\n              return handle(entry.catchLoc, true);\n            } else if (this.prev < entry.finallyLoc) {\n              return handle(entry.finallyLoc);\n            }\n\n          } else if (hasCatch) {\n            if (this.prev < entry.catchLoc) {\n              return handle(entry.catchLoc, true);\n            }\n\n          } else if (hasFinally) {\n            if (this.prev < entry.finallyLoc) {\n              return handle(entry.finallyLoc);\n            }\n\n          } else {\n            throw new Error(\"try statement without catch or finally\");\n          }\n        }\n      }\n    },\n\n    abrupt: function(type, arg) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.tryLoc <= this.prev &&\n            hasOwn.call(entry, \"finallyLoc\") &&\n            this.prev < entry.finallyLoc) {\n          var finallyEntry = entry;\n          break;\n        }\n      }\n\n      if (finallyEntry &&\n          (type === \"break\" ||\n           type === \"continue\") &&\n          finallyEntry.tryLoc <= arg &&\n          arg <= finallyEntry.finallyLoc) {\n        // Ignore the finally entry if control is not jumping to a\n        // location outside the try/catch block.\n        finallyEntry = null;\n      }\n\n      var record = finallyEntry ? finallyEntry.completion : {};\n      record.type = type;\n      record.arg = arg;\n\n      if (finallyEntry) {\n        this.method = \"next\";\n        this.next = finallyEntry.finallyLoc;\n        return ContinueSentinel;\n      }\n\n      return this.complete(record);\n    },\n\n    complete: function(record, afterLoc) {\n      if (record.type === \"throw\") {\n        throw record.arg;\n      }\n\n      if (record.type === \"break\" ||\n          record.type === \"continue\") {\n        this.next = record.arg;\n      } else if (record.type === \"return\") {\n        this.rval = this.arg = record.arg;\n        this.method = \"return\";\n        this.next = \"end\";\n      } else if (record.type === \"normal\" && afterLoc) {\n        this.next = afterLoc;\n      }\n\n      return ContinueSentinel;\n    },\n\n    finish: function(finallyLoc) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.finallyLoc === finallyLoc) {\n          this.complete(entry.completion, entry.afterLoc);\n          resetTryEntry(entry);\n          return ContinueSentinel;\n        }\n      }\n    },\n\n    \"catch\": function(tryLoc) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.tryLoc === tryLoc) {\n          var record = entry.completion;\n          if (record.type === \"throw\") {\n            var thrown = record.arg;\n            resetTryEntry(entry);\n          }\n          return thrown;\n        }\n      }\n\n      // The context.catch method must only be called with a location\n      // argument that corresponds to a known catch block.\n      throw new Error(\"illegal catch attempt\");\n    },\n\n    delegateYield: function(iterable, resultName, nextLoc) {\n      this.delegate = {\n        iterator: values(iterable),\n        resultName: resultName,\n        nextLoc: nextLoc\n      };\n\n      if (this.method === \"next\") {\n        // Deliberately forget the last sent value so that we don't\n        // accidentally pass it on to the delegate.\n        this.arg = undefined;\n      }\n\n      return ContinueSentinel;\n    }\n  };\n\n  // Regardless of whether this script is executing as a CommonJS module\n  // or not, return the runtime object so that we can declare the variable\n  // regeneratorRuntime in the outer scope, which allows this module to be\n  // injected easily by `bin/regenerator --include-runtime script.js`.\n  return exports;\n\n}(\n  // If this script is executing as a CommonJS module, use module.exports\n  // as the regeneratorRuntime namespace. Otherwise create a new empty\n  // object. Either way, the resulting object will be used to initialize\n  // the regeneratorRuntime variable at the top of this file.\n  typeof module === \"object\" ? module.exports : {}\n));\n\ntry {\n  regeneratorRuntime = runtime;\n} catch (accidentalStrictMode) {\n  // This module should not be running in strict mode, so the above\n  // assignment should always work unless something is misconfigured. Just\n  // in case runtime.js accidentally runs in strict mode, we can escape\n  // strict mode using a global Function call. This could conceivably fail\n  // if a Content Security Policy forbids using Function, but in that case\n  // the proper solution is to fix the accidental strict mode problem. If\n  // you've misconfigured your bundler to force strict mode and applied a\n  // CSP to forbid Function, and you're not willing to fix either of those\n  // problems, please detail your unique predicament in a GitHub issue.\n  Function(\"r\", \"regeneratorRuntime = r\")(runtime);\n}\n","import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\n\nexport function ucscProcessedTranscript(feature: Feature) {\n  const children = feature.children()\n  // split the blocks into UTR, CDS, and exons\n  const thickStart = feature.get('thickStart')\n  const thickEnd = feature.get('thickEnd')\n\n  if (!thickStart && !thickEnd) {\n    return feature\n  }\n\n  const blocks: Feature[] = children\n    ? children\n        .filter(child => child.get('type') === 'block')\n        .sort((a, b) => a.get('start') - b.get('start'))\n    : []\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  const newChildren: Record<string, any> = []\n  blocks.forEach(block => {\n    const start = block.get('start')\n    const end = block.get('end')\n    if (thickStart >= end) {\n      // left-side UTR\n      const prime = feature.get('strand') > 0 ? 'five' : 'three'\n      newChildren.push({\n        type: `${prime}_prime_UTR`,\n        start,\n        end,\n      })\n    } else if (thickStart > start && thickStart < end && thickEnd >= end) {\n      // UTR | CDS\n      const prime = feature.get('strand') > 0 ? 'five' : 'three'\n      newChildren.push(\n        {\n          type: `${prime}_prime_UTR`,\n          start,\n          end: thickStart,\n        },\n        {\n          type: 'CDS',\n          start: thickStart,\n          end,\n        },\n      )\n    } else if (thickStart <= start && thickEnd >= end) {\n      // CDS\n      newChildren.push({\n        type: 'CDS',\n        start,\n        end,\n      })\n    } else if (thickStart > start && thickStart < end && thickEnd < end) {\n      // UTR | CDS | UTR\n      const leftPrime = feature.get('strand') > 0 ? 'five' : 'three'\n      const rightPrime = feature.get('strand') > 0 ? 'three' : 'five'\n      newChildren.push(\n        {\n          type: `${leftPrime}_prime_UTR`,\n          start,\n          end: thickStart,\n        },\n        {\n          type: `CDS`,\n          start: thickStart,\n          end: thickEnd,\n        },\n        {\n          type: `${rightPrime}_prime_UTR`,\n          start: thickEnd,\n          end,\n        },\n      )\n    } else if (thickStart <= start && thickEnd > start && thickEnd < end) {\n      // CDS | UTR\n      const prime = feature.get('strand') > 0 ? 'three' : 'five'\n      newChildren.push(\n        {\n          type: `CDS`,\n          start,\n          end: thickEnd,\n        },\n        {\n          type: `${prime}_prime_UTR`,\n          start: thickEnd,\n          end,\n        },\n      )\n    } else if (thickEnd <= start) {\n      // right-side UTR\n      const prime = feature.get('strand') > 0 ? 'three' : 'five'\n      newChildren.push({\n        type: `${prime}_prime_UTR`,\n        start,\n        end,\n      })\n    }\n  })\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  const newData: Record<string, any> = {}\n  feature.tags().forEach(tag => {\n    newData[tag] = feature.get(tag)\n  })\n  newData.subfeatures = newChildren\n  newData.type = 'mRNA'\n  newData.uniqueId = feature.id()\n  delete newData.chromStarts\n  delete newData.chromStart\n  delete newData.chromEnd\n  delete newData.chrom\n  delete newData.blockStarts\n  delete newData.blockSizes\n  delete newData.blockCount\n  delete newData.thickStart\n  delete newData.thickEnd\n  const newFeature = new SimpleFeature({\n    data: newData,\n    id: feature.id(),\n  })\n  return newFeature\n}\n","/* eslint-disable @typescript-eslint/no-explicit-any */\nimport { BigBed } from '@gmod/bbi'\nimport BED from '@gmod/bed'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { Region, FileLocation } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { map, mergeAll } from 'rxjs/operators'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { Instance } from 'mobx-state-tree'\nimport configSchema from './configSchema'\nimport { ucscProcessedTranscript } from '../util'\n\ninterface BEDFeature {\n  chrom: string\n  chromStart: number\n  chromEnd: number\n  [key: string]: any\n}\n\ninterface Parser {\n  parseLine: (line: string, opts: { uniqueId: string | number }) => BEDFeature\n}\n\nexport default class BigBedAdapter extends BaseFeatureDataAdapter {\n  private bigbed: BigBed\n\n  private parser: Promise<Parser>\n\n  public constructor(config: Instance<typeof configSchema>) {\n    super(config)\n    const bigBedLocation = readConfObject(\n      config,\n      'bigBedLocation',\n    ) as FileLocation\n    this.bigbed = new BigBed({\n      filehandle: openLocation(bigBedLocation),\n    })\n\n    this.parser = this.bigbed\n      .getHeader()\n      .then(({ autoSql }: { autoSql: string }) => new BED({ autoSql }))\n  }\n\n  public async getRefNames() {\n    return Object.keys((await this.bigbed.getHeader()).refsByName)\n  }\n\n  async getHeader(opts?: BaseOptions) {\n    const { version, fileType } = await this.bigbed.getHeader(opts)\n    // @ts-ignore\n    const { autoSql } = await this.parser\n    const { fields, ...rest } = autoSql\n    const f = Object.fromEntries(\n      // @ts-ignore\n      fields.map(({ name, comment }) => [name, comment]),\n    )\n    return { version, fileType, autoSql: { ...rest }, fields: f }\n  }\n\n  public async refIdToName(refId: number) {\n    return ((await this.bigbed.getHeader()).refsByNumber[refId] || {}).name\n  }\n\n  public getFeatures(region: Region, opts: BaseOptions = {}) {\n    const { refName, start, end } = region\n    const { signal } = opts\n    return ObservableCreate<Feature>(async observer => {\n      try {\n        const parser = await this.parser\n        const ob = await this.bigbed.getFeatureStream(refName, start, end, {\n          signal,\n          basesPerSpan: end - start,\n        })\n        ob.pipe(\n          mergeAll(),\n          map(\n            (r: {\n              start: number\n              end: number\n              rest?: string\n              uniqueId?: string\n            }) => {\n              const data = parser.parseLine(\n                `${refName}\\t${r.start}\\t${r.end}\\t${r.rest}`,\n                {\n                  uniqueId: r.uniqueId as string,\n                },\n              )\n\n              const { blockCount, blockSizes, blockStarts, chromStarts } = data\n              if (blockCount) {\n                const starts = chromStarts || blockStarts || []\n                const sizes = blockSizes\n                const blocksOffset = r.start\n                data.subfeatures = []\n\n                for (let b = 0; b < blockCount; b += 1) {\n                  const bmin = (starts[b] || 0) + blocksOffset\n                  const bmax = bmin + (sizes[b] || 0)\n                  data.subfeatures.push({\n                    uniqueId: `${r.uniqueId}-${b}`,\n                    start: bmin,\n                    end: bmax,\n                    type: 'block',\n                  })\n                }\n              }\n              if (r.uniqueId === undefined) {\n                throw new Error('invalid bbi feature')\n              }\n              delete data.chromStart\n              delete data.chromEnd\n              delete data.chrom\n\n              const f = new SimpleFeature({\n                id: `${this.id}-${r.uniqueId}`,\n                data: {\n                  ...data,\n                  start: r.start,\n                  end: r.end,\n                  refName,\n                },\n              })\n\n              // collection of heuristics for suggesting that this feature\n              // should be converted to a gene, CNV bigbed has many gene like\n              // features including thickStart and blockCount but no strand\n              return f.get('thickStart') &&\n                f.get('blockCount') &&\n                f.get('strand') !== 0\n                ? ucscProcessedTranscript(f)\n                : f\n            },\n          ),\n        ).subscribe(observer)\n      } catch (e) {\n        observer.error(e)\n      }\n    }, opts.signal)\n  }\n\n  public freeResources(): void {}\n}\n","/* eslint-disable @typescript-eslint/no-explicit-any */\nimport BED from '@gmod/bed'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { FileLocation, Region } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { TabixIndexedFile } from '@gmod/tabix'\nimport { Instance } from 'mobx-state-tree'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { ucscProcessedTranscript } from '../util'\nimport MyConfigSchema from './configSchema'\n\nexport default class BedTabixAdapter extends BaseFeatureDataAdapter {\n  private parser: any\n\n  protected bed: TabixIndexedFile\n\n  protected columnNames: string[]\n\n  protected scoreColumn: string\n\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  public constructor(config: Instance<typeof MyConfigSchema>) {\n    super(config)\n    const bedGzLocation = readConfObject(\n      config,\n      'bedGzLocation',\n    ) as FileLocation\n    const index = readConfObject(config, 'index') as {\n      indexType?: string\n      location: FileLocation\n    }\n    const autoSql = readConfObject(config, 'autoSql') as string\n    const { location, indexType } = index\n\n    this.bed = new TabixIndexedFile({\n      filehandle: openLocation(bedGzLocation),\n      csiFilehandle: indexType === 'CSI' ? openLocation(location) : undefined,\n      tbiFilehandle: indexType !== 'CSI' ? openLocation(location) : undefined,\n      chunkCacheSize: 50 * 2 ** 20,\n    })\n    this.columnNames = readConfObject(config, 'columnNames')\n    this.scoreColumn = readConfObject(config, 'scoreColumn')\n    this.parser = new BED({ autoSql })\n  }\n\n  public async getRefNames(opts: BaseOptions = {}) {\n    return this.bed.getReferenceSequenceNames(opts)\n  }\n\n  async getHeader() {\n    return this.bed.getHeader()\n  }\n\n  defaultParser(fields: string[], line: string) {\n    return Object.fromEntries(line.split('\\t').map((f, i) => [fields[i], f]))\n  }\n\n  async getNames() {\n    if (this.columnNames.length) {\n      return this.columnNames\n    }\n    const header = await this.bed.getHeader()\n    const defs = header.split('\\n').filter(f => !!f)\n    const defline = defs[defs.length - 1]\n    return defline && defline.includes('\\t')\n      ? defline\n          .slice(1)\n          .split('\\t')\n          .map(field => field.trim())\n      : null\n  }\n\n  public getFeatures(query: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const meta = await this.bed.getMetadata()\n      const { columnNumbers } = meta\n      const colRef = columnNumbers.ref - 1\n      const colStart = columnNumbers.start - 1\n      const colEnd = columnNumbers.end - 1\n      // colSame handles special case for tabix where a single column is both\n      // the start and end, this is assumed to be covering the base at this\n      // position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same\n      const colSame = colStart === colEnd ? 1 : 0\n      const names = await this.getNames()\n      await this.bed.getLines(query.refName, query.start, query.end, {\n        lineCallback: (line: string, fileOffset: number) => {\n          const l = line.split('\\t')\n          const refName = l[colRef]\n          const start = +l[colStart]\n\n          const end = +l[colEnd] + colSame\n          const uniqueId = `${this.id}-${fileOffset}`\n          const data = names\n            ? this.defaultParser(names, line)\n            : this.parser.parseLine(line, { uniqueId })\n\n          const { blockCount, blockSizes, blockStarts, chromStarts } = data\n\n          if (blockCount) {\n            const starts = chromStarts || blockStarts || []\n            const sizes = blockSizes\n            const blocksOffset = start\n            data.subfeatures = []\n\n            for (let b = 0; b < blockCount; b += 1) {\n              const bmin = (starts[b] || 0) + blocksOffset\n              const bmax = bmin + (sizes[b] || 0)\n              data.subfeatures.push({\n                uniqueId: `${uniqueId}-${b}`,\n                start: bmin,\n                end: bmax,\n 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+{"version":3,"file":"plugin-bed.cjs.production.min.js","sources":["../src/BigBedAdapter/configSchema.ts","../src/BedTabixAdapter/configSchema.ts","../src/index.ts","../../../node_modules/regenerator-runtime/runtime.js","../src/util.ts","../src/BigBedAdapter/BigBedAdapter.ts","../src/BedTabixAdapter/BedTabixAdapter.ts"],"sourcesContent":["import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'BigBedAdapter',\n  {\n    bigBedLocation: {\n      type: 'fileLocation',\n      defaultValue: { uri: '/path/to/my.bb', locationType: 'UriLocation' },\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default ConfigurationSchema(\n  'BedTabixAdapter',\n  {\n    bedGzLocation: {\n      type: 'fileLocation',\n      defaultValue: { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' },\n    },\n\n    index: ConfigurationSchema('TabixIndex', {\n      indexType: {\n        model: types.enumeration('IndexType', ['TBI', 'CSI']),\n        type: 'stringEnum',\n        defaultValue: 'TBI',\n      },\n      location: {\n        type: 'fileLocation',\n        defaultValue: {\n          uri: '/path/to/my.bed.gz.tbi',\n          locationType: 'UriLocation',\n        },\n      },\n    }),\n\n    columnNames: {\n      type: 'stringArray',\n      description: 'List of column names',\n      defaultValue: [],\n    },\n\n    scoreColumn: {\n      type: 'string',\n      description: 'The column to use as a \"score\" attribute',\n      defaultValue: '',\n    },\n\n    autoSql: {\n      type: 'string',\n      description: 'The autoSql definition for the data fields in the file',\n      defaultValue: '',\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { configSchema as bigBedAdapterConfigSchema } from './BigBedAdapter'\nimport { configSchema as bedTabixAdapterConfigSchema } from './BedTabixAdapter'\nimport { FileLocation } from '@jbrowse/core/util/types'\nimport {\n  makeIndex,\n  makeIndexType,\n  AdapterGuesser,\n  getFileName,\n} from '@jbrowse/core/util/tracks'\n\nexport default class BedPlugin extends Plugin {\n  name = 'BedPlugin'\n\n  install(pluginManager: PluginManager) {\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'BigBedAdapter',\n          configSchema: bigBedAdapterConfigSchema,\n          getAdapterClass: () =>\n            import('./BigBedAdapter/BigBedAdapter').then(r => r.default),\n        }),\n    )\n    pluginManager.addToExtensionPoint(\n      'Core-guessAdapterForLocation',\n      (adapterGuesser: AdapterGuesser) => {\n        return (\n          file: FileLocation,\n          index?: FileLocation,\n          adapterHint?: string,\n        ) => {\n          const regexGuess = /\\.(bb|bigbed)$/i\n          const adapterName = 'BigBedAdapter'\n          const fileName = getFileName(file)\n          if (regexGuess.test(fileName) || adapterHint === adapterName) {\n            return {\n              type: adapterName,\n              bigBedLocation: file,\n            }\n          }\n          return adapterGuesser(file, index, adapterHint)\n        }\n      },\n    )\n\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'BedTabixAdapter',\n          configSchema: bedTabixAdapterConfigSchema,\n          getAdapterClass: () =>\n            import('./BedTabixAdapter/BedTabixAdapter').then(r => r.default),\n        }),\n    )\n    pluginManager.addToExtensionPoint(\n      'Core-guessAdapterForLocation',\n      (adapterGuesser: AdapterGuesser) => {\n        return (\n          file: FileLocation,\n          index?: FileLocation,\n          adapterHint?: string,\n        ) => {\n          const regexGuess = /\\.bed\\.b?gz$/i\n          const adapterName = 'BedTabixAdapter'\n          const fileName = getFileName(file)\n          const indexName = index && getFileName(index)\n          if (regexGuess.test(fileName) || adapterHint === adapterName) {\n            return {\n              type: adapterName,\n              bedGzLocation: file,\n              index: {\n                location: index || makeIndex(file, '.tbi'),\n                indexType: makeIndexType(indexName, 'CSI', 'TBI'),\n              },\n            }\n          }\n          return adapterGuesser(file, index, adapterHint)\n        }\n      },\n    )\n  }\n}\n","/**\n * Copyright (c) 2014-present, Facebook, Inc.\n *\n * This source code is licensed under the MIT license found in the\n * LICENSE file in the root directory of this source tree.\n */\n\nvar runtime = (function (exports) {\n  \"use strict\";\n\n  var Op = Object.prototype;\n  var hasOwn = Op.hasOwnProperty;\n  var undefined; // More compressible than void 0.\n  var $Symbol = typeof Symbol === \"function\" ? Symbol : {};\n  var iteratorSymbol = $Symbol.iterator || \"@@iterator\";\n  var asyncIteratorSymbol = $Symbol.asyncIterator || \"@@asyncIterator\";\n  var toStringTagSymbol = $Symbol.toStringTag || \"@@toStringTag\";\n\n  function define(obj, key, value) {\n    Object.defineProperty(obj, key, {\n      value: value,\n      enumerable: true,\n      configurable: true,\n      writable: true\n    });\n    return obj[key];\n  }\n  try {\n    // IE 8 has a broken Object.defineProperty that only works on DOM objects.\n    define({}, \"\");\n  } catch (err) {\n    define = function(obj, key, value) {\n      return obj[key] = value;\n    };\n  }\n\n  function wrap(innerFn, outerFn, self, tryLocsList) {\n    // If outerFn provided and outerFn.prototype is a Generator, then outerFn.prototype instanceof Generator.\n    var protoGenerator = outerFn && outerFn.prototype instanceof Generator ? outerFn : Generator;\n    var generator = Object.create(protoGenerator.prototype);\n    var context = new Context(tryLocsList || []);\n\n    // The ._invoke method unifies the implementations of the .next,\n    // .throw, and .return methods.\n    generator._invoke = makeInvokeMethod(innerFn, self, context);\n\n    return generator;\n  }\n  exports.wrap = wrap;\n\n  // Try/catch helper to minimize deoptimizations. Returns a completion\n  // record like context.tryEntries[i].completion. This interface could\n  // have been (and was previously) designed to take a closure to be\n  // invoked without arguments, but in all the cases we care about we\n  // already have an existing method we want to call, so there's no need\n  // to create a new function object. We can even get away with assuming\n  // the method takes exactly one argument, since that happens to be true\n  // in every case, so we don't have to touch the arguments object. The\n  // only additional allocation required is the completion record, which\n  // has a stable shape and so hopefully should be cheap to allocate.\n  function tryCatch(fn, obj, arg) {\n    try {\n      return { type: \"normal\", arg: fn.call(obj, arg) };\n    } catch (err) {\n      return { type: \"throw\", arg: err };\n    }\n  }\n\n  var GenStateSuspendedStart = \"suspendedStart\";\n  var GenStateSuspendedYield = \"suspendedYield\";\n  var GenStateExecuting = \"executing\";\n  var GenStateCompleted = \"completed\";\n\n  // Returning this object from the innerFn has the same effect as\n  // breaking out of the dispatch switch statement.\n  var ContinueSentinel = {};\n\n  // Dummy constructor functions that we use as the .constructor and\n  // .constructor.prototype properties for functions that return Generator\n  // objects. For full spec compliance, you may wish to configure your\n  // minifier not to mangle the names of these two functions.\n  function Generator() {}\n  function GeneratorFunction() {}\n  function GeneratorFunctionPrototype() {}\n\n  // This is a polyfill for %IteratorPrototype% for environments that\n  // don't natively support it.\n  var IteratorPrototype = {};\n  define(IteratorPrototype, iteratorSymbol, function () {\n    return this;\n  });\n\n  var getProto = Object.getPrototypeOf;\n  var NativeIteratorPrototype = getProto && getProto(getProto(values([])));\n  if (NativeIteratorPrototype &&\n      NativeIteratorPrototype !== Op &&\n      hasOwn.call(NativeIteratorPrototype, iteratorSymbol)) {\n    // This environment has a native %IteratorPrototype%; use it instead\n    // of the polyfill.\n    IteratorPrototype = NativeIteratorPrototype;\n  }\n\n  var Gp = GeneratorFunctionPrototype.prototype =\n    Generator.prototype = Object.create(IteratorPrototype);\n  GeneratorFunction.prototype = GeneratorFunctionPrototype;\n  define(Gp, \"constructor\", GeneratorFunctionPrototype);\n  define(GeneratorFunctionPrototype, \"constructor\", GeneratorFunction);\n  GeneratorFunction.displayName = define(\n    GeneratorFunctionPrototype,\n    toStringTagSymbol,\n    \"GeneratorFunction\"\n  );\n\n  // Helper for defining the .next, .throw, and .return methods of the\n  // Iterator interface in terms of a single ._invoke method.\n  function defineIteratorMethods(prototype) {\n    [\"next\", \"throw\", \"return\"].forEach(function(method) {\n      define(prototype, method, function(arg) {\n        return this._invoke(method, arg);\n      });\n    });\n  }\n\n  exports.isGeneratorFunction = function(genFun) {\n    var ctor = typeof genFun === \"function\" && genFun.constructor;\n    return ctor\n      ? ctor === GeneratorFunction ||\n        // For the native GeneratorFunction constructor, the best we can\n        // do is to check its .name property.\n        (ctor.displayName || ctor.name) === \"GeneratorFunction\"\n      : false;\n  };\n\n  exports.mark = function(genFun) {\n    if (Object.setPrototypeOf) {\n      Object.setPrototypeOf(genFun, GeneratorFunctionPrototype);\n    } else {\n      genFun.__proto__ = GeneratorFunctionPrototype;\n      define(genFun, toStringTagSymbol, \"GeneratorFunction\");\n    }\n    genFun.prototype = Object.create(Gp);\n    return genFun;\n  };\n\n  // Within the body of any async function, `await x` is transformed to\n  // `yield regeneratorRuntime.awrap(x)`, so that the runtime can test\n  // `hasOwn.call(value, \"__await\")` to determine if the yielded value is\n  // meant to be awaited.\n  exports.awrap = function(arg) {\n    return { __await: arg };\n  };\n\n  function AsyncIterator(generator, PromiseImpl) {\n    function invoke(method, arg, resolve, reject) {\n      var record = tryCatch(generator[method], generator, arg);\n      if (record.type === \"throw\") {\n        reject(record.arg);\n      } else {\n        var result = record.arg;\n        var value = result.value;\n        if (value &&\n            typeof value === \"object\" &&\n            hasOwn.call(value, \"__await\")) {\n          return PromiseImpl.resolve(value.__await).then(function(value) {\n            invoke(\"next\", value, resolve, reject);\n          }, function(err) {\n            invoke(\"throw\", err, resolve, reject);\n          });\n        }\n\n        return PromiseImpl.resolve(value).then(function(unwrapped) {\n          // When a yielded Promise is resolved, its final value becomes\n          // the .value of the Promise<{value,done}> result for the\n          // current iteration.\n          result.value = unwrapped;\n          resolve(result);\n        }, function(error) {\n          // If a rejected Promise was yielded, throw the rejection back\n          // into the async generator function so it can be handled there.\n          return invoke(\"throw\", error, resolve, reject);\n        });\n      }\n    }\n\n    var previousPromise;\n\n    function enqueue(method, arg) {\n      function callInvokeWithMethodAndArg() {\n        return new PromiseImpl(function(resolve, reject) {\n          invoke(method, arg, resolve, reject);\n        });\n      }\n\n      return previousPromise =\n        // If enqueue has been called before, then we want to wait until\n        // all previous Promises have been resolved before calling invoke,\n        // so that results are always delivered in the correct order. If\n        // enqueue has not been called before, then it is important to\n        // call invoke immediately, without waiting on a callback to fire,\n        // so that the async generator function has the opportunity to do\n        // any necessary setup in a predictable way. This predictability\n        // is why the Promise constructor synchronously invokes its\n        // executor callback, and why async functions synchronously\n        // execute code before the first await. Since we implement simple\n        // async functions in terms of async generators, it is especially\n        // important to get this right, even though it requires care.\n        previousPromise ? previousPromise.then(\n          callInvokeWithMethodAndArg,\n          // Avoid propagating failures to Promises returned by later\n          // invocations of the iterator.\n          callInvokeWithMethodAndArg\n        ) : callInvokeWithMethodAndArg();\n    }\n\n    // Define the unified helper method that is used to implement .next,\n    // .throw, and .return (see defineIteratorMethods).\n    this._invoke = enqueue;\n  }\n\n  defineIteratorMethods(AsyncIterator.prototype);\n  define(AsyncIterator.prototype, asyncIteratorSymbol, function () {\n    return this;\n  });\n  exports.AsyncIterator = AsyncIterator;\n\n  // Note that simple async functions are implemented on top of\n  // AsyncIterator objects; they just return a Promise for the value of\n  // the final result produced by the iterator.\n  exports.async = function(innerFn, outerFn, self, tryLocsList, PromiseImpl) {\n    if (PromiseImpl === void 0) PromiseImpl = Promise;\n\n    var iter = new AsyncIterator(\n      wrap(innerFn, outerFn, self, tryLocsList),\n      PromiseImpl\n    );\n\n    return exports.isGeneratorFunction(outerFn)\n      ? iter // If outerFn is a generator, return the full iterator.\n      : iter.next().then(function(result) {\n          return result.done ? result.value : iter.next();\n        });\n  };\n\n  function makeInvokeMethod(innerFn, self, context) {\n    var state = GenStateSuspendedStart;\n\n    return function invoke(method, arg) {\n      if (state === GenStateExecuting) {\n        throw new Error(\"Generator is already running\");\n      }\n\n      if (state === GenStateCompleted) {\n        if (method === \"throw\") {\n          throw arg;\n        }\n\n        // Be forgiving, per 25.3.3.3.3 of the spec:\n        // https://people.mozilla.org/~jorendorff/es6-draft.html#sec-generatorresume\n        return doneResult();\n      }\n\n      context.method = method;\n      context.arg = arg;\n\n      while (true) {\n        var delegate = context.delegate;\n        if (delegate) {\n          var delegateResult = maybeInvokeDelegate(delegate, context);\n          if (delegateResult) {\n            if (delegateResult === ContinueSentinel) continue;\n            return delegateResult;\n          }\n        }\n\n        if (context.method === \"next\") {\n          // Setting context._sent for legacy support of Babel's\n          // function.sent implementation.\n          context.sent = context._sent = context.arg;\n\n        } else if (context.method === \"throw\") {\n          if (state === GenStateSuspendedStart) {\n            state = GenStateCompleted;\n            throw context.arg;\n          }\n\n          context.dispatchException(context.arg);\n\n        } else if (context.method === \"return\") {\n          context.abrupt(\"return\", context.arg);\n        }\n\n        state = GenStateExecuting;\n\n        var record = tryCatch(innerFn, self, context);\n        if (record.type === \"normal\") {\n          // If an exception is thrown from innerFn, we leave state ===\n          // GenStateExecuting and loop back for another invocation.\n          state = context.done\n            ? GenStateCompleted\n            : GenStateSuspendedYield;\n\n          if (record.arg === ContinueSentinel) {\n            continue;\n          }\n\n          return {\n            value: record.arg,\n            done: context.done\n          };\n\n        } else if (record.type === \"throw\") {\n          state = GenStateCompleted;\n          // Dispatch the exception by looping back around to the\n          // context.dispatchException(context.arg) call above.\n          context.method = \"throw\";\n          context.arg = record.arg;\n        }\n      }\n    };\n  }\n\n  // Call delegate.iterator[context.method](context.arg) and handle the\n  // result, either by returning a { value, done } result from the\n  // delegate iterator, or by modifying context.method and context.arg,\n  // setting context.delegate to null, and returning the ContinueSentinel.\n  function maybeInvokeDelegate(delegate, context) {\n    var method = delegate.iterator[context.method];\n    if (method === undefined) {\n      // A .throw or .return when the delegate iterator has no .throw\n      // method always terminates the yield* loop.\n      context.delegate = null;\n\n      if (context.method === \"throw\") {\n        // Note: [\"return\"] must be used for ES3 parsing compatibility.\n        if (delegate.iterator[\"return\"]) {\n          // If the delegate iterator has a return method, give it a\n          // chance to clean up.\n          context.method = \"return\";\n          context.arg = undefined;\n          maybeInvokeDelegate(delegate, context);\n\n          if (context.method === \"throw\") {\n            // If maybeInvokeDelegate(context) changed context.method from\n            // \"return\" to \"throw\", let that override the TypeError below.\n            return ContinueSentinel;\n          }\n        }\n\n        context.method = \"throw\";\n        context.arg = new TypeError(\n          \"The iterator does not provide a 'throw' method\");\n      }\n\n      return ContinueSentinel;\n    }\n\n    var record = tryCatch(method, delegate.iterator, context.arg);\n\n    if (record.type === \"throw\") {\n      context.method = \"throw\";\n      context.arg = record.arg;\n      context.delegate = null;\n      return ContinueSentinel;\n    }\n\n    var info = record.arg;\n\n    if (! info) {\n      context.method = \"throw\";\n      context.arg = new TypeError(\"iterator result is not an object\");\n      context.delegate = null;\n      return ContinueSentinel;\n    }\n\n    if (info.done) {\n      // Assign the result of the finished delegate to the temporary\n      // variable specified by delegate.resultName (see delegateYield).\n      context[delegate.resultName] = info.value;\n\n      // Resume execution at the desired location (see delegateYield).\n      context.next = delegate.nextLoc;\n\n      // If context.method was \"throw\" but the delegate handled the\n      // exception, let the outer generator proceed normally. If\n      // context.method was \"next\", forget context.arg since it has been\n      // \"consumed\" by the delegate iterator. If context.method was\n      // \"return\", allow the original .return call to continue in the\n      // outer generator.\n      if (context.method !== \"return\") {\n        context.method = \"next\";\n        context.arg = undefined;\n      }\n\n    } else {\n      // Re-yield the result returned by the delegate method.\n      return info;\n    }\n\n    // The delegate iterator is finished, so forget it and continue with\n    // the outer generator.\n    context.delegate = null;\n    return ContinueSentinel;\n  }\n\n  // Define Generator.prototype.{next,throw,return} in terms of the\n  // unified ._invoke helper method.\n  defineIteratorMethods(Gp);\n\n  define(Gp, toStringTagSymbol, \"Generator\");\n\n  // A Generator should always return itself as the iterator object when the\n  // @@iterator function is called on it. Some browsers' implementations of the\n  // iterator prototype chain incorrectly implement this, causing the Generator\n  // object to not be returned from this call. This ensures that doesn't happen.\n  // See https://github.com/facebook/regenerator/issues/274 for more details.\n  define(Gp, iteratorSymbol, function() {\n    return this;\n  });\n\n  define(Gp, \"toString\", function() {\n    return \"[object Generator]\";\n  });\n\n  function pushTryEntry(locs) {\n    var entry = { tryLoc: locs[0] };\n\n    if (1 in locs) {\n      entry.catchLoc = locs[1];\n    }\n\n    if (2 in locs) {\n      entry.finallyLoc = locs[2];\n      entry.afterLoc = locs[3];\n    }\n\n    this.tryEntries.push(entry);\n  }\n\n  function resetTryEntry(entry) {\n    var record = entry.completion || {};\n    record.type = \"normal\";\n    delete record.arg;\n    entry.completion = record;\n  }\n\n  function Context(tryLocsList) {\n    // The root entry object (effectively a try statement without a catch\n    // or a finally block) gives us a place to store values thrown from\n    // locations where there is no enclosing try statement.\n    this.tryEntries = [{ tryLoc: \"root\" }];\n    tryLocsList.forEach(pushTryEntry, this);\n    this.reset(true);\n  }\n\n  exports.keys = function(object) {\n    var keys = [];\n    for (var key in object) {\n      keys.push(key);\n    }\n    keys.reverse();\n\n    // Rather than returning an object with a next method, we keep\n    // things simple and return the next function itself.\n    return function next() {\n      while (keys.length) {\n        var key = keys.pop();\n        if (key in object) {\n          next.value = key;\n          next.done = false;\n          return next;\n        }\n      }\n\n      // To avoid creating an additional object, we just hang the .value\n      // and .done properties off the next function object itself. This\n      // also ensures that the minifier will not anonymize the function.\n      next.done = true;\n      return next;\n    };\n  };\n\n  function values(iterable) {\n    if (iterable) {\n      var iteratorMethod = iterable[iteratorSymbol];\n      if (iteratorMethod) {\n        return iteratorMethod.call(iterable);\n      }\n\n      if (typeof iterable.next === \"function\") {\n        return iterable;\n      }\n\n      if (!isNaN(iterable.length)) {\n        var i = -1, next = function next() {\n          while (++i < iterable.length) {\n            if (hasOwn.call(iterable, i)) {\n              next.value = iterable[i];\n              next.done = false;\n              return next;\n            }\n          }\n\n          next.value = undefined;\n          next.done = true;\n\n          return next;\n        };\n\n        return next.next = next;\n      }\n    }\n\n    // Return an iterator with no values.\n    return { next: doneResult };\n  }\n  exports.values = values;\n\n  function doneResult() {\n    return { value: undefined, done: true };\n  }\n\n  Context.prototype = {\n    constructor: Context,\n\n    reset: function(skipTempReset) {\n      this.prev = 0;\n      this.next = 0;\n      // Resetting context._sent for legacy support of Babel's\n      // function.sent implementation.\n      this.sent = this._sent = undefined;\n      this.done = false;\n      this.delegate = null;\n\n      this.method = \"next\";\n      this.arg = undefined;\n\n      this.tryEntries.forEach(resetTryEntry);\n\n      if (!skipTempReset) {\n        for (var name in this) {\n          // Not sure about the optimal order of these conditions:\n          if (name.charAt(0) === \"t\" &&\n              hasOwn.call(this, name) &&\n              !isNaN(+name.slice(1))) {\n            this[name] = undefined;\n          }\n        }\n      }\n    },\n\n    stop: function() {\n      this.done = true;\n\n      var rootEntry = this.tryEntries[0];\n      var rootRecord = rootEntry.completion;\n      if (rootRecord.type === \"throw\") {\n        throw rootRecord.arg;\n      }\n\n      return this.rval;\n    },\n\n    dispatchException: function(exception) {\n      if (this.done) {\n        throw exception;\n      }\n\n      var context = this;\n      function handle(loc, caught) {\n        record.type = \"throw\";\n        record.arg = exception;\n        context.next = loc;\n\n        if (caught) {\n          // If the dispatched exception was caught by a catch block,\n          // then let that catch block handle the exception normally.\n          context.method = \"next\";\n          context.arg = undefined;\n        }\n\n        return !! caught;\n      }\n\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        var record = entry.completion;\n\n        if (entry.tryLoc === \"root\") {\n          // Exception thrown outside of any try block that could handle\n          // it, so set the completion value of the entire function to\n          // throw the exception.\n          return handle(\"end\");\n        }\n\n        if (entry.tryLoc <= this.prev) {\n          var hasCatch = hasOwn.call(entry, \"catchLoc\");\n          var hasFinally = hasOwn.call(entry, \"finallyLoc\");\n\n          if (hasCatch && hasFinally) {\n            if (this.prev < entry.catchLoc) {\n              return handle(entry.catchLoc, true);\n            } else if (this.prev < entry.finallyLoc) {\n              return handle(entry.finallyLoc);\n            }\n\n          } else if (hasCatch) {\n            if (this.prev < entry.catchLoc) {\n              return handle(entry.catchLoc, true);\n            }\n\n          } else if (hasFinally) {\n            if (this.prev < entry.finallyLoc) {\n              return handle(entry.finallyLoc);\n            }\n\n          } else {\n            throw new Error(\"try statement without catch or finally\");\n          }\n        }\n      }\n    },\n\n    abrupt: function(type, arg) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.tryLoc <= this.prev &&\n            hasOwn.call(entry, \"finallyLoc\") &&\n            this.prev < entry.finallyLoc) {\n          var finallyEntry = entry;\n          break;\n        }\n      }\n\n      if (finallyEntry &&\n          (type === \"break\" ||\n           type === \"continue\") &&\n          finallyEntry.tryLoc <= arg &&\n          arg <= finallyEntry.finallyLoc) {\n        // Ignore the finally entry if control is not jumping to a\n        // location outside the try/catch block.\n        finallyEntry = null;\n      }\n\n      var record = finallyEntry ? finallyEntry.completion : {};\n      record.type = type;\n      record.arg = arg;\n\n      if (finallyEntry) {\n        this.method = \"next\";\n        this.next = finallyEntry.finallyLoc;\n        return ContinueSentinel;\n      }\n\n      return this.complete(record);\n    },\n\n    complete: function(record, afterLoc) {\n      if (record.type === \"throw\") {\n        throw record.arg;\n      }\n\n      if (record.type === \"break\" ||\n          record.type === \"continue\") {\n        this.next = record.arg;\n      } else if (record.type === \"return\") {\n        this.rval = this.arg = record.arg;\n        this.method = \"return\";\n        this.next = \"end\";\n      } else if (record.type === \"normal\" && afterLoc) {\n        this.next = afterLoc;\n      }\n\n      return ContinueSentinel;\n    },\n\n    finish: function(finallyLoc) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.finallyLoc === finallyLoc) {\n          this.complete(entry.completion, entry.afterLoc);\n          resetTryEntry(entry);\n          return ContinueSentinel;\n        }\n      }\n    },\n\n    \"catch\": function(tryLoc) {\n      for (var i = this.tryEntries.length - 1; i >= 0; --i) {\n        var entry = this.tryEntries[i];\n        if (entry.tryLoc === tryLoc) {\n          var record = entry.completion;\n          if (record.type === \"throw\") {\n            var thrown = record.arg;\n            resetTryEntry(entry);\n          }\n          return thrown;\n        }\n      }\n\n      // The context.catch method must only be called with a location\n      // argument that corresponds to a known catch block.\n      throw new Error(\"illegal catch attempt\");\n    },\n\n    delegateYield: function(iterable, resultName, nextLoc) {\n      this.delegate = {\n        iterator: values(iterable),\n        resultName: resultName,\n        nextLoc: nextLoc\n      };\n\n      if (this.method === \"next\") {\n        // Deliberately forget the last sent value so that we don't\n        // accidentally pass it on to the delegate.\n        this.arg = undefined;\n      }\n\n      return ContinueSentinel;\n    }\n  };\n\n  // Regardless of whether this script is executing as a CommonJS module\n  // or not, return the runtime object so that we can declare the variable\n  // regeneratorRuntime in the outer scope, which allows this module to be\n  // injected easily by `bin/regenerator --include-runtime script.js`.\n  return exports;\n\n}(\n  // If this script is executing as a CommonJS module, use module.exports\n  // as the regeneratorRuntime namespace. Otherwise create a new empty\n  // object. Either way, the resulting object will be used to initialize\n  // the regeneratorRuntime variable at the top of this file.\n  typeof module === \"object\" ? module.exports : {}\n));\n\ntry {\n  regeneratorRuntime = runtime;\n} catch (accidentalStrictMode) {\n  // This module should not be running in strict mode, so the above\n  // assignment should always work unless something is misconfigured. Just\n  // in case runtime.js accidentally runs in strict mode, in modern engines\n  // we can explicitly access globalThis. In older engines we can escape\n  // strict mode using a global Function call. This could conceivably fail\n  // if a Content Security Policy forbids using Function, but in that case\n  // the proper solution is to fix the accidental strict mode problem. If\n  // you've misconfigured your bundler to force strict mode and applied a\n  // CSP to forbid Function, and you're not willing to fix either of those\n  // problems, please detail your unique predicament in a GitHub issue.\n  if (typeof globalThis === \"object\") {\n    globalThis.regeneratorRuntime = runtime;\n  } else {\n    Function(\"r\", \"regeneratorRuntime = r\")(runtime);\n  }\n}\n","import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\n\nexport function ucscProcessedTranscript(feature: Feature) {\n  const children = feature.children()\n  // split the blocks into UTR, CDS, and exons\n  const thickStart = feature.get('thickStart')\n  const thickEnd = feature.get('thickEnd')\n\n  if (!thickStart && !thickEnd) {\n    return feature\n  }\n\n  const blocks: Feature[] = children\n    ? children\n        .filter(child => child.get('type') === 'block')\n        .sort((a, b) => a.get('start') - b.get('start'))\n    : []\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  const newChildren: Record<string, any> = []\n  blocks.forEach(block => {\n    const start = block.get('start')\n    const end = block.get('end')\n    if (thickStart >= end) {\n      // left-side UTR\n      const prime = feature.get('strand') > 0 ? 'five' : 'three'\n      newChildren.push({\n        type: `${prime}_prime_UTR`,\n        start,\n        end,\n      })\n    } else if (thickStart > start && thickStart < end && thickEnd >= end) {\n      // UTR | CDS\n      const prime = feature.get('strand') > 0 ? 'five' : 'three'\n      newChildren.push(\n        {\n          type: `${prime}_prime_UTR`,\n          start,\n          end: thickStart,\n        },\n        {\n          type: 'CDS',\n          start: thickStart,\n          end,\n        },\n      )\n    } else if (thickStart <= start && thickEnd >= end) {\n      // CDS\n      newChildren.push({\n        type: 'CDS',\n        start,\n        end,\n      })\n    } else if (thickStart > start && thickStart < end && thickEnd < end) {\n      // UTR | CDS | UTR\n      const leftPrime = feature.get('strand') > 0 ? 'five' : 'three'\n      const rightPrime = feature.get('strand') > 0 ? 'three' : 'five'\n      newChildren.push(\n        {\n          type: `${leftPrime}_prime_UTR`,\n          start,\n          end: thickStart,\n        },\n        {\n          type: `CDS`,\n          start: thickStart,\n          end: thickEnd,\n        },\n        {\n          type: `${rightPrime}_prime_UTR`,\n          start: thickEnd,\n          end,\n        },\n      )\n    } else if (thickStart <= start && thickEnd > start && thickEnd < end) {\n      // CDS | UTR\n      const prime = feature.get('strand') > 0 ? 'three' : 'five'\n      newChildren.push(\n        {\n          type: `CDS`,\n          start,\n          end: thickEnd,\n        },\n        {\n          type: `${prime}_prime_UTR`,\n          start: thickEnd,\n          end,\n        },\n      )\n    } else if (thickEnd <= start) {\n      // right-side UTR\n      const prime = feature.get('strand') > 0 ? 'three' : 'five'\n      newChildren.push({\n        type: `${prime}_prime_UTR`,\n        start,\n        end,\n      })\n    }\n  })\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  const newData: Record<string, any> = {}\n  feature.tags().forEach(tag => {\n    newData[tag] = feature.get(tag)\n  })\n  newData.subfeatures = newChildren\n  newData.type = 'mRNA'\n  newData.uniqueId = feature.id()\n  delete newData.chromStarts\n  delete newData.chromStart\n  delete newData.chromEnd\n  delete newData.chrom\n  delete newData.blockStarts\n  delete newData.blockSizes\n  delete newData.blockCount\n  delete newData.thickStart\n  delete newData.thickEnd\n  const newFeature = new SimpleFeature({\n    data: newData,\n    id: feature.id(),\n  })\n  return newFeature\n}\n","/* eslint-disable @typescript-eslint/no-explicit-any */\nimport { BigBed } from '@gmod/bbi'\nimport BED from '@gmod/bed'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { Region, FileLocation } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { map, mergeAll } from 'rxjs/operators'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { Instance } from 'mobx-state-tree'\nimport configSchema from './configSchema'\nimport { ucscProcessedTranscript } from '../util'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\ninterface BEDFeature {\n  chrom: string\n  chromStart: number\n  chromEnd: number\n  [key: string]: any\n}\n\ninterface Parser {\n  parseLine: (line: string, opts: { uniqueId: string | number }) => BEDFeature\n}\n\nexport default class BigBedAdapter extends BaseFeatureDataAdapter {\n  private bigbed: BigBed\n\n  private parser: Promise<Parser>\n\n  public constructor(\n    config: Instance<typeof configSchema>,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const bigBedLocation = readConfObject(\n      config,\n      'bigBedLocation',\n    ) as FileLocation\n    this.bigbed = new BigBed({\n      filehandle: openLocation(bigBedLocation, this.pluginManager),\n    })\n\n    this.parser = this.bigbed\n      .getHeader()\n      .then(({ autoSql }: { autoSql: string }) => new BED({ autoSql }))\n  }\n\n  public async getRefNames() {\n    return Object.keys((await this.bigbed.getHeader()).refsByName)\n  }\n\n  async getHeader(opts?: BaseOptions) {\n    const { version, fileType } = await this.bigbed.getHeader(opts)\n    // @ts-ignore\n    const { autoSql } = await this.parser\n    const { fields, ...rest } = autoSql\n    const f = Object.fromEntries(\n      // @ts-ignore\n      fields.map(({ name, comment }) => [name, comment]),\n    )\n    return { version, fileType, autoSql: { ...rest }, fields: f }\n  }\n\n  public async refIdToName(refId: number) {\n    return ((await this.bigbed.getHeader()).refsByNumber[refId] || {}).name\n  }\n\n  public getFeatures(region: Region, opts: BaseOptions = {}) {\n    const { refName, start, end } = region\n    const { signal } = opts\n    return ObservableCreate<Feature>(async observer => {\n      try {\n        const parser = await this.parser\n        const ob = await this.bigbed.getFeatureStream(refName, start, end, {\n          signal,\n          basesPerSpan: end - start,\n        })\n        ob.pipe(\n          mergeAll(),\n          map(\n            (r: {\n              start: number\n              end: number\n              rest?: string\n              uniqueId?: string\n            }) => {\n              const data = parser.parseLine(\n                `${refName}\\t${r.start}\\t${r.end}\\t${r.rest}`,\n                {\n                  uniqueId: r.uniqueId as string,\n                },\n              )\n\n              const { blockCount, blockSizes, blockStarts, chromStarts } = data\n              if (blockCount) {\n                const starts = chromStarts || blockStarts || []\n                const sizes = blockSizes\n                const blocksOffset = r.start\n                data.subfeatures = []\n\n                for (let b = 0; b < blockCount; b += 1) {\n                  const bmin = (starts[b] || 0) + blocksOffset\n                  const bmax = bmin + (sizes[b] || 0)\n                  data.subfeatures.push({\n                    uniqueId: `${r.uniqueId}-${b}`,\n                    start: bmin,\n                    end: bmax,\n                    type: 'block',\n                  })\n                }\n              }\n              if (r.uniqueId === undefined) {\n                throw new Error('invalid bbi feature')\n              }\n              const { chromStart, chromEnd, chrom, ...rest } = data\n\n              const f = new SimpleFeature({\n                id: `${this.id}-${r.uniqueId}`,\n                data: {\n                  ...rest,\n                  start: r.start,\n                  end: r.end,\n                  refName,\n                },\n              })\n\n              // collection of heuristics for suggesting that this feature\n              // should be converted to a gene, CNV bigbed has many gene like\n              // features including thickStart and blockCount but no strand\n              return f.get('thickStart') &&\n                f.get('blockCount') &&\n                f.get('strand') !== 0\n                ? ucscProcessedTranscript(f)\n                : f\n            },\n          ),\n        ).subscribe(observer)\n      } catch (e) {\n        observer.error(e)\n      }\n    }, opts.signal)\n  }\n\n  public freeResources(): void {}\n}\n","/* eslint-disable @typescript-eslint/no-explicit-any */\nimport BED from '@gmod/bed'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { FileLocation, Region } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { TabixIndexedFile } from '@gmod/tabix'\nimport { Instance } from 'mobx-state-tree'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { ucscProcessedTranscript } from '../util'\nimport MyConfigSchema from './configSchema'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\nexport default class BedTabixAdapter extends BaseFeatureDataAdapter {\n  private parser: any\n\n  protected bed: TabixIndexedFile\n\n  protected columnNames: string[]\n\n  protected scoreColumn: string\n\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  public constructor(\n    config: Instance<typeof MyConfigSchema>,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const bedGzLocation = readConfObject(\n      config,\n      'bedGzLocation',\n    ) as FileLocation\n    const index = readConfObject(config, 'index') as {\n      indexType?: string\n      location: FileLocation\n    }\n    const autoSql = readConfObject(config, 'autoSql') as string\n    const { location, indexType } = index\n\n    this.bed = new TabixIndexedFile({\n      filehandle: openLocation(bedGzLocation, this.pluginManager),\n      csiFilehandle:\n        indexType === 'CSI'\n          ? openLocation(location, this.pluginManager)\n          : undefined,\n      tbiFilehandle:\n        indexType !== 'CSI'\n          ? openLocation(location, this.pluginManager)\n          : undefined,\n      chunkCacheSize: 50 * 2 ** 20,\n    })\n    this.columnNames = readConfObject(config, 'columnNames')\n    this.scoreColumn = readConfObject(config, 'scoreColumn')\n    this.parser = new BED({ autoSql })\n  }\n\n  public async getRefNames(opts: BaseOptions = {}) {\n    return this.bed.getReferenceSequenceNames(opts)\n  }\n\n  async getHeader() {\n    return this.bed.getHeader()\n  }\n\n  defaultParser(fields: string[], line: string) {\n    return Object.fromEntries(line.split('\\t').map((f, i) => [fields[i], f]))\n  }\n\n  async getNames() {\n    if (this.columnNames.length) {\n      return this.columnNames\n    }\n    const header = await this.bed.getHeader()\n    const defs = header.split('\\n').filter(f => !!f)\n    const defline = defs[defs.length - 1]\n    return defline && defline.includes('\\t')\n      ? defline\n          .slice(1)\n          .split('\\t')\n          .map(field => field.trim())\n      : null\n  }\n\n  public getFeatures(query: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const meta = await this.bed.getMetadata()\n      const { columnNumbers } = meta\n      const colRef = columnNumbers.ref - 1\n      const colStart = columnNumbers.start - 1\n      const colEnd = columnNumbers.end - 1\n      // colSame handles special case for tabix where a single column is both\n      // the start and end, this is assumed to be covering the base at this\n      // position (e.g. tabix -s 1 -b 2 -e 2) begin and end are same\n      const colSame = colStart === colEnd ? 1 : 0\n      const names = await this.getNames()\n      await this.bed.getLines(query.refName, query.start, query.end, {\n        lineCallback: (line: string, fileOffset: number) => {\n          const l = line.split('\\t')\n          const refName = l[colRef]\n          const start = +l[colStart]\n\n          const end = +l[colEnd] + colSame\n          const uniqueId = `${this.id}-${fileOffset}`\n          const data = names\n            ? this.defaultParser(names, line)\n            : this.parser.parseLine(line, { uniqueId })\n\n          const { blockCount, blockSizes, blockStarts, chromStarts } = data\n\n          if (blockCount) {\n            const starts = chromStarts || blockStarts || []\n            const sizes = blockSizes\n            const blocksOffset = start\n            data.subfeatures = []\n\n            for (let b = 0; b < blockCount; b += 1) {\n              const bmin = (starts[b] || 0) + blocksOffset\n              const bmax = bmin + (sizes[b] || 0)\n              data.subfeatures.push({\n                uniqueId: `${uniqueId}-${b}`,\n                start: bmin,\n                end: bmax,\n                type: 'block',\n              })\n            }\n          }\n\n          if (this.scoreColumn) {\n            data.score = data[this.scoreColumn]\n          }\n          delete data.chrom\n          delete data.chromStart\n          delete data.chromEnd\n          const f = new SimpleFeature({\n            ...data,\n            start,\n       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package/dist/plugin-bed.esm.js

@@ -2,6 +2,7 @@ import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import Plugin from '@jbrowse/core/Plugin';
 import { ConfigurationSchema, readConfObject } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
+import { getFileName, makeIndex, makeIndexType } from '@jbrowse/core/util/tracks';
 import { BigBed } from '@gmod/bbi';
 import BED from '@gmod/bed';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
@@ -213,6 +214,8 @@ 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);
@@ -241,7 +244,8 @@ var bigBedAdapterConfigSchema = /*#__PURE__*/ConfigurationSchema('BigBedAdapter'
   bigBedLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/my.bb'
+      uri: '/path/to/my.bb',
+      locationType: 'UriLocation'
     }
   }
 }, {
@@ -252,7 +256,8 @@ var bedTabixAdapterConfigSchema = /*#__PURE__*/ConfigurationSchema('BedTabixAdap
   bedGzLocation: {
     type: 'fileLocation',
     defaultValue: {
-      uri: '/path/to/my.bed.gz'
+      uri: '/path/to/my.bed.gz',
+      locationType: 'UriLocation'
     }
   },
   index: /*#__PURE__*/ConfigurationSchema('TabixIndex', {
@@ -264,7 +269,8 @@ var bedTabixAdapterConfigSchema = /*#__PURE__*/ConfigurationSchema('BedTabixAdap
     location: {
       type: 'fileLocation',
       defaultValue: {
-        uri: '/path/to/my.bed.gz.tbi'
+        uri: '/path/to/my.bed.gz.tbi',
+        locationType: 'UriLocation'
       }
     }
   }),
@@ -316,6 +322,22 @@ var BedPlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.(bb|bigbed)$/i;
+          var adapterName = 'BigBedAdapter';
+          var fileName = getFileName(file);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bigBedLocation: file
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
       pluginManager.addAdapterType(function () {
         return new AdapterType({
           name: 'BedTabixAdapter',
@@ -327,6 +349,27 @@ var BedPlugin = /*#__PURE__*/function (_Plugin) {
           }
         });
       });
+      pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', function (adapterGuesser) {
+        return function (file, index, adapterHint) {
+          var regexGuess = /\.bed\.b?gz$/i;
+          var adapterName = 'BedTabixAdapter';
+          var fileName = getFileName(file);
+          var indexName = index && getFileName(index);
+
+          if (regexGuess.test(fileName) || adapterHint === adapterName) {
+            return {
+              type: adapterName,
+              bedGzLocation: file,
+              index: {
+                location: index || makeIndex(file, '.tbi'),
+                indexType: makeIndexType(indexName, 'CSI', 'TBI')
+              }
+            };
+          }
+
+          return adapterGuesser(file, index, adapterHint);
+        };
+      });
     }
   }]);
 
@@ -430,11 +473,9 @@ 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([])));
 
@@ -445,8 +486,9 @@ 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.
 
@@ -551,11 +593,9 @@ 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.
@@ -732,13 +772,12 @@ 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 = {
@@ -1050,14 +1089,19 @@ 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);
+    }
   }
 });
 
@@ -1175,22 +1219,23 @@ 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 = readConfObject(config, 'bigBedLocation');
     _this.bigbed = new BigBed({
-      filehandle: openLocation(bigBedLocation)
+      filehandle: openLocation(bigBedLocation, _this.pluginManager)
     });
     _this.parser = _this.bigbed.getHeader().then(function (_ref) {
       var autoSql = _ref.autoSql;
@@ -1383,12 +1428,11 @@ 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
@@ -1438,21 +1482,21 @@ 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 = readConfObject(config, 'bedGzLocation');
     var index = readConfObject(config, 'index');
     var autoSql = readConfObject(config, 'autoSql');
     var location = index.location,
         indexType = index.indexType;
     _this.bed = new TabixIndexedFile({
-      filehandle: openLocation(bedGzLocation),
-      csiFilehandle: indexType === 'CSI' ? openLocation(location) : undefined,
-      tbiFilehandle: indexType !== 'CSI' ? openLocation(location) : undefined,
+      filehandle: openLocation(bedGzLocation, _this.pluginManager),
+      csiFilehandle: indexType === 'CSI' ? openLocation(location, _this.pluginManager) : undefined,
+      tbiFilehandle: indexType !== 'CSI' ? openLocation(location, _this.pluginManager) : undefined,
       chunkCacheSize: 50 * Math.pow(2, 20)
     });
     _this.columnNames = readConfObject(config, 'columnNames');