@jbrowse/plugin-variants 1.4.3 → 1.5.2

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

@@ -1 +1 @@
-{"version":3,"file":"plugin-variants.cjs.development.js","sources":["../src/ChordVariantDisplay/models/ChordVariantDisplay.js","../src/ChordVariantDisplay/index.ts","../src/LinearVariantDisplay/configSchema.ts","../../../node_modules/regenerator-runtime/runtime.js","../src/LinearVariantDisplay/model.ts","../src/StructuralVariantChordRenderer/ReactComponent.js","../src/StructuralVariantChordRenderer/index.js","../src/VariantFeatureWidget/index.js","../src/VcfTabixAdapter/configSchema.ts","../src/VcfAdapter/configSchema.ts","../src/VcfTabixAdapter/VcfFeature.ts","../src/index.ts","../src/VcfTabixAdapter/VcfTabixAdapter.ts","../src/VcfAdapter/VcfAdapter.ts","../src/VariantFeatureWidget/BreakendOptionDialog.tsx","../src/VariantFeatureWidget/VariantFeatureWidget.tsx"],"sourcesContent":["import {\n  baseChordDisplayConfig,\n  BaseChordDisplayModel,\n} from '@jbrowse/plugin-circular-view'\n\nconst ChordVariantDisplayF = pluginManager => {\n  const { jbrequire } = pluginManager\n\n  const { types } = jbrequire('mobx-state-tree')\n  const { ConfigurationSchema, ConfigurationReference } = jbrequire(\n    '@jbrowse/core/configuration',\n  )\n  const { getContainingView } = jbrequire('@jbrowse/core/util')\n  const { getParentRenderProps } = jbrequire('@jbrowse/core/util/tracks')\n  const configSchema = ConfigurationSchema(\n    'ChordVariantDisplay',\n    {\n      renderer: types.optional(\n        pluginManager.pluggableConfigSchemaType('renderer'),\n        { type: 'StructuralVariantChordRenderer' },\n      ),\n    },\n    { baseConfiguration: baseChordDisplayConfig, explicitlyTyped: true },\n  )\n\n  const stateModel = types\n    .compose(\n      'ChordVariantDisplay',\n      BaseChordDisplayModel,\n      types.model({\n        type: types.literal('ChordVariantDisplay'),\n        configuration: ConfigurationReference(configSchema),\n      }),\n    )\n    .views(self => ({\n      get rendererTypeName() {\n        return self.configuration.renderer.type\n      },\n\n      renderProps() {\n        const view = getContainingView(self)\n        return {\n          ...getParentRenderProps(self),\n          rpcDriverName: self.rpcDriverName,\n          displayModel: self,\n          bezierRadius: view.radiusPx * self.bezierRadiusRatio,\n          radius: view.radiusPx,\n          blockDefinitions: this.blockDefinitions,\n          config: self.configuration.renderer,\n          onChordClick: self.onChordClick,\n        }\n      },\n    }))\n\n  return { stateModel, configSchema }\n}\n\n// http://localhost:3000/test_data/hs37d5.HG002-SequelII-CCS.sv.vcf.gz.tbi\n\n// render request is for 1.5x the current viewing window\n\n// tracks all have a height\n//\nexport default ChordVariantDisplayF\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport { BaseChordDisplayComponentFactory } from '@jbrowse/plugin-circular-view'\nimport ChordVariantDisplay from './models/ChordVariantDisplay'\n\nexport default (pluginManager: PluginManager) => {\n  const { lib, load } = pluginManager\n  const DisplayType = lib['@jbrowse/core/pluggableElementTypes/DisplayType']\n\n  const { stateModel, configSchema } = load(ChordVariantDisplay)\n\n  return new DisplayType({\n    name: 'ChordVariantDisplay',\n    configSchema,\n    stateModel,\n    trackType: 'VariantTrack',\n    viewType: 'CircularView',\n    ReactComponent: BaseChordDisplayComponentFactory(pluginManager),\n  })\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { Instance } from 'mobx-state-tree'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view'\n\nexport function LinearVariantDisplayConfigFactory(\n  pluginManager: PluginManager,\n) {\n  const configSchema = linearBasicDisplayConfigSchemaFactory(pluginManager)\n\n  return ConfigurationSchema(\n    'LinearVariantDisplay',\n    {},\n    { baseConfiguration: configSchema, explicitlyTyped: true },\n  )\n}\n\nexport type LinearVariantDisplayConfigModel = ReturnType<\n  typeof LinearVariantDisplayConfigFactory\n>\nexport type LinearVariantDisplayConfig = Instance<LinearVariantDisplayConfigModel>\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 { getConf, ConfigurationReference } from '@jbrowse/core/configuration'\nimport { getRpcSessionId } from '@jbrowse/core/util/tracks'\nimport {\n  getContainingTrack,\n  getSession,\n  getContainingView,\n  isSessionModelWithWidgets,\n} from '@jbrowse/core/util'\n\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view'\nimport { types } from 'mobx-state-tree'\nimport { LinearVariantDisplayConfigModel } from './configSchema'\n\nexport default function (configSchema: LinearVariantDisplayConfigModel) {\n  return types\n    .compose(\n      'LinearVariantDisplay',\n      linearBasicDisplayModelFactory(configSchema),\n      types.model({\n        type: types.literal('LinearVariantDisplay'),\n        configuration: ConfigurationReference(configSchema),\n      }),\n    )\n    .actions(self => ({\n      async selectFeature(feature: Feature) {\n        const session = getSession(self)\n        if (isSessionModelWithWidgets(session)) {\n          const { rpcManager } = session\n          const sessionId = getRpcSessionId(self)\n          const track = getContainingTrack(self)\n          const adapterConfig = getConf(track, 'adapter')\n          const header = await rpcManager.call(sessionId, 'CoreGetMetadata', {\n            adapterConfig,\n          })\n          const featureWidget = session.addWidget(\n            'VariantFeatureWidget',\n            'variantFeature',\n            {\n              featureData: feature.toJSON(),\n              view: getContainingView(self),\n              descriptions: header,\n            },\n          )\n          session.showWidget(featureWidget)\n        }\n\n        session.setSelection(feature)\n      },\n    }))\n}\n","import React, { useMemo } from 'react'\nimport { observer, PropTypes as MobxPropTypes } from 'mobx-react'\nimport { polarToCartesian } from '@jbrowse/core/util'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { PropTypes as CommonPropTypes } from '@jbrowse/core/util/types/mst'\nimport { parseBreakend } from '@gmod/vcf'\nimport PropTypes from 'prop-types'\n\nfunction bpToRadians(block, pos) {\n  const blockStart = block.region.elided ? 0 : block.region.start\n  const blockEnd = block.region.elided ? 0 : block.region.end\n  const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart\n  const radians = bpOffset / block.bpPerRadian + block.startRadians\n  return radians\n}\n\nconst Chord = observer(function Chord({\n  feature,\n  blocksForRefs,\n  radius,\n  config,\n  bezierRadius,\n  selected,\n  onClick,\n}) {\n  // find the blocks that our start and end points belong to\n  const startBlock = blocksForRefs[feature.get('refName')]\n  if (!startBlock) {\n    return null\n  }\n  let svType\n  if (feature.get('INFO')) {\n    ;[svType] = feature.get('INFO').SVTYPE || []\n  } else if (feature.get('mate')) {\n    svType = 'mate'\n  }\n  let endPosition\n  let endBlock\n  const alt = feature.get('ALT')?.[0]\n  const bnd = parseBreakend(alt)\n  if (bnd) {\n    // VCF BND\n    const matePosition = bnd.MatePosition.split(':')\n    endPosition = +matePosition[1]\n    endBlock = blocksForRefs[matePosition[0]]\n  } else if (alt === '<TRA>') {\n    // VCF TRA\n    const chr2 = feature.get('INFO')?.CHR2?.[0]\n    const end = feature.get('INFO')?.END?.[0]\n    endPosition = parseInt(end, 10)\n    endBlock = blocksForRefs[chr2]\n  } else if (svType === 'mate') {\n    // generic simplefeatures arcs\n    const mate = feature.get('mate')\n    const chr2 = mate.refName\n    endPosition = mate.start\n    endBlock = blocksForRefs[chr2]\n  }\n\n  if (endBlock) {\n    const startPos = feature.get('start')\n    const startRadians = bpToRadians(startBlock, startPos)\n    const endRadians = bpToRadians(endBlock, endPosition)\n    const startXY = polarToCartesian(radius, startRadians)\n    const endXY = polarToCartesian(radius, endRadians)\n    const controlXY = polarToCartesian(\n      bezierRadius,\n      (endRadians + startRadians) / 2,\n    )\n\n    const strokeColor = selected\n      ? readConfObject(config, 'strokeColorSelected', { feature })\n      : readConfObject(config, 'strokeColor', { feature })\n\n    const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {\n      feature,\n    })\n    return (\n      <path\n        data-testid={`chord-${feature.id()}`}\n        d={['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' ')}\n        style={{ stroke: strokeColor }}\n        onClick={evt =>\n          onClick(feature, startBlock.region, endBlock.region, evt)\n        }\n        onMouseOver={evt => {\n          if (!selected) {\n            evt.target.style.stroke = hoverStrokeColor\n            evt.target.style.strokeWidth = 3\n          }\n        }}\n        onMouseOut={evt => {\n          if (!selected) {\n            evt.target.style.stroke = strokeColor\n          }\n        }}\n      />\n    )\n  }\n\n  return null\n})\n\nfunction StructuralVariantChords(props) {\n  const {\n    features,\n    config,\n    displayModel,\n    blockDefinitions,\n    radius,\n    bezierRadius,\n    displayModel: { selectedFeatureId },\n\n    onChordClick,\n  } = props\n  // make a map of refName -> blockDefinition\n  const blocksForRefsMemo = useMemo(() => {\n    const blocksForRefs = {}\n    blockDefinitions.forEach(block => {\n      const regions = block.region.elided\n        ? block.region.regions\n        : [block.region]\n      regions.forEach(region => {\n        blocksForRefs[region.refName] = block\n      })\n    })\n    return blocksForRefs\n  }, [blockDefinitions])\n  // console.log(blocksForRefs)\n  const chords = []\n  for (const [id, feature] of features) {\n    const selected = String(selectedFeatureId) === String(feature.id())\n    chords.push(\n      <Chord\n        key={id}\n        feature={feature}\n        config={config}\n        displayModel={displayModel}\n        radius={radius}\n        bezierRadius={bezierRadius}\n        blocksForRefs={blocksForRefsMemo}\n        selected={selected}\n        onClick={onChordClick}\n      />,\n    )\n  }\n  const trackStyleId = `chords-${displayModel.id}`\n  return (\n    <g id={trackStyleId} data-testid=\"structuralVariantChordRenderer\">\n      <style\n        // eslint-disable-next-line react/no-danger\n        dangerouslySetInnerHTML={{\n          __html: `\n          #${trackStyleId} > path {\n            cursor: crosshair;\n            fill: none;\n          }\n`,\n        }}\n      />\n      {chords}\n    </g>\n  )\n}\n\nStructuralVariantChords.propTypes = {\n  features: PropTypes.instanceOf(Map).isRequired,\n  config: CommonPropTypes.ConfigSchema.isRequired,\n  displayModel: MobxPropTypes.objectOrObservableObject,\n  blockDefinitions: PropTypes.arrayOf(MobxPropTypes.objectOrObservableObject)\n    .isRequired,\n  radius: PropTypes.number.isRequired,\n  bezierRadius: PropTypes.number.isRequired,\n  selectedFeatureId: PropTypes.string,\n  onChordClick: PropTypes.oneOfType([PropTypes.func, PropTypes.string]),\n}\n\nStructuralVariantChords.defaultProps = {\n  displayModel: undefined,\n  selectedFeatureId: '',\n  onChordClick: undefined,\n}\n\nexport default observer(StructuralVariantChords)\n","import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport ReactComponent from './ReactComponent'\n\nconst ChordRendererConfigF = pluginManager => {\n  const configSchema = ConfigurationSchema(\n    'StructuralVariantChordRenderer',\n    {\n      strokeColor: {\n        type: 'color',\n        description: 'the line color of each arc',\n        defaultValue: 'rgba(255,133,0,0.32)',\n        contextVariable: ['feature'],\n      },\n      strokeColorSelected: {\n        type: 'color',\n        description: 'the line color of an arc that has been selected',\n        defaultValue: 'black',\n        contextVariable: ['feature'],\n      },\n      strokeColorHover: {\n        type: 'color',\n        description:\n          'the line color of an arc that is being hovered over with the mouse',\n        defaultValue: '#555',\n        contextVariable: ['feature'],\n      },\n    },\n    { explicitlyTyped: true },\n  )\n  return new ChordRendererType({\n    name: 'StructuralVariantChordRenderer',\n    ReactComponent,\n    configSchema,\n    pluginManager,\n  })\n}\n\nexport default ChordRendererConfigF\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { ElementId } from '@jbrowse/core/util/types/mst'\nimport { types } from 'mobx-state-tree'\n\nexport const configSchema = ConfigurationSchema('VariantFeatureWidget', {})\n\nexport function stateModelFactory(pluginManager) {\n  return types\n    .model('VariantFeatureWidget', {\n      id: ElementId,\n      type: types.literal('VariantFeatureWidget'),\n      view: types.safeReference(\n        pluginManager.pluggableMstType('view', 'stateModel'),\n      ),\n      featureData: types.frozen(),\n      descriptions: types.frozen(),\n    })\n    .actions(self => ({\n      setFeatureData(data) {\n        self.featureData = data\n      },\n      clearFeatureData() {\n        self.featureData = undefined\n      },\n    }))\n}\n","import { types } from 'mobx-state-tree'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'VcfTabixAdapter',\n  {\n    vcfGzLocation: {\n      type: 'fileLocation',\n      defaultValue: { uri: '/path/to/my.vcf.gz' },\n    },\n    index: ConfigurationSchema('VcfIndex', {\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.vcf.gz.tbi' },\n      },\n    }),\n  },\n  { explicitlyTyped: true },\n)\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'VcfAdapter',\n  {\n    vcfLocation: {\n      type: 'fileLocation',\n      defaultValue: { uri: '/path/to/my.vcf' },\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { parseBreakend } from '@gmod/vcf'\n\n/* eslint-disable no-underscore-dangle */\n\n/**\n * VCF Feature creation with lazy genotype evaluation.\n */\ninterface Samples {\n  [key: string]: {\n    [key: string]: { values: string[] | number[] | null }\n  }\n}\n\ninterface FeatureData {\n  [key: string]: unknown\n  refName: string\n  start: number\n  end: number\n  description?: string\n  type?: string\n  name?: string\n  aliases?: string[]\n  samples?: Samples\n}\n\nexport default class VCFFeature implements Feature {\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  private variant: any\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  private parser: any\n\n  private data: FeatureData\n\n  private _id: string\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  constructor(args: { variant: any; parser: any; id: string }) {\n    this.variant = args.variant\n    this.parser = args.parser\n    this.data = this.dataFromVariant(this.variant)\n    this._id = args.id\n  }\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  get(field: string): any {\n    return field === 'samples'\n      ? this.variant.SAMPLES\n      : this.data[field] || this.variant[field]\n  }\n\n  set(): void {}\n\n  parent(): undefined {\n    return undefined\n  }\n\n  children(): undefined {\n    return undefined\n  }\n\n  tags(): string[] {\n    const t = [\n      ...Object.keys(this.data),\n      ...Object.keys(this.variant),\n      'samples',\n    ]\n    return t\n  }\n\n  id(): string {\n    return this._id\n  }\n\n  dataFromVariant(variant: {\n    REF: string\n    POS: number\n    ALT: string[]\n    CHROM: string\n    INFO: any // eslint-disable-line @typescript-eslint/no-explicit-any\n    ID: string[]\n  }): FeatureData {\n    const { REF, ALT, POS, CHROM, INFO, ID } = variant\n    const start = POS - 1\n    const [SO_term, description] = this._getSOTermAndDescription(REF, ALT)\n    const isTRA = ALT?.some(f => f === '<TRA>')\n    const isSymbolic = ALT?.some(f => f.indexOf('<') !== -1)\n\n    return {\n      refName: CHROM,\n      start,\n      end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,\n      description,\n      type: SO_term,\n      name: ID?.join(','),\n      aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,\n    }\n  }\n\n  /**\n   * Get a sequence ontology (SO) term that describes the variant type\n   */\n  _getSOTermAndDescription(\n    ref: string,\n    alt: string[],\n  ): [string, string] | [undefined, undefined] {\n    // it's just a remark if there are no alternate alleles\n    if (!alt || alt === []) {\n      return ['remark', 'no alternative alleles']\n    }\n\n    const soTerms = new Set<string>()\n    let descriptions = new Set<string>()\n    alt.forEach(a => {\n      let [soTerm, description] = this._getSOAndDescFromAltDefs(ref, a)\n\n      if (!soTerm) {\n        ;[soTerm, description] = this._getSOAndDescByExamination(ref, a)\n      }\n      if (soTerm && description) {\n        soTerms.add(soTerm)\n        descriptions.add(description)\n      }\n    })\n\n    // Combine descriptions like [\"SNV G -> A\", \"SNV G -> T\"] to [\"SNV G -> A,T\"]\n    if (descriptions.size > 1) {\n      const prefixes = new Set(\n        [...descriptions].map(desc => {\n          const prefix = desc.split('->')\n          return prefix[1] ? prefix[0] : desc\n        }),\n      )\n\n      const new_descs = [...prefixes].map(prefix => {\n        const suffixes = [...descriptions]\n          .map(desc => {\n            const pref = desc.split('-> ')\n            return pref[1] && pref[0] === prefix ? pref[1] : ''\n          })\n          .filter(f => !!f)\n\n        return suffixes.length\n          ? prefix + '-> ' + suffixes.join(',')\n          : [...descriptions].join(',')\n      })\n\n      descriptions = new Set(new_descs)\n    }\n    if (soTerms.size) {\n      return [[...soTerms].join(','), [...descriptions].join(',')]\n    }\n    return [undefined, undefined]\n  }\n\n  static _altTypeToSO: { [key: string]: string | undefined } = {\n    DEL: 'deletion',\n    INS: 'insertion',\n    DUP: 'duplication',\n    INV: 'inversion',\n    INVDUP: 'inverted duplication',\n    CNV: 'copy_number_variation',\n    TRA: 'translocation',\n    'DUP:TANDEM': 'tandem_duplication',\n    NON_REF: 'sequence_variant',\n    '*': 'sequence_variant',\n  }\n\n  _getSOAndDescFromAltDefs(\n    ref: string,\n    alt: string,\n  ): [string, string] | [undefined, undefined] {\n    if (typeof alt === 'string' && !alt.startsWith('<')) {\n      return [undefined, undefined]\n    }\n\n    // look for a definition with an SO type for this\n    let soTerm = VCFFeature._altTypeToSO[alt]\n    // if no SO term but ALT is in metadata, assume sequence_variant\n    if (!soTerm && this.parser.getMetadata('ALT', alt)) {\n      soTerm = 'sequence_variant'\n    }\n    if (soTerm) {\n      return [soTerm, alt]\n    }\n\n    // try to look for a definition for a parent term if we can\n    const modAlt = alt.split(':')\n    if (modAlt.length > 1) {\n      return this._getSOAndDescFromAltDefs(\n        ref,\n        `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`,\n      )\n    }\n\n    // no parent\n    return [undefined, undefined]\n  }\n\n  // note: term SNV is used instead of SNP because SO definition of SNP says\n  // abundance must be at least 1% in population, and can't be sure we meet\n  // that\n  _getSOAndDescByExamination(ref: string, alt: string): [string, string] {\n    const bnd = parseBreakend(alt)\n    if (bnd) {\n      return ['breakend', alt]\n    } else if (ref.length === 1 && alt.length === 1) {\n      return ['SNV', this._makeDescriptionString('SNV', ref, alt)]\n    } else if (alt === '<INS>') {\n      return ['insertion', alt]\n    } else if (alt === '<DEL>') {\n      return ['deletion', alt]\n    } else if (alt === '<INV>') {\n      return ['deletion', alt]\n    } else if (alt === '<TRA>') {\n      return ['translocation', alt]\n    } else if (alt.includes('<')) {\n      return ['sv', alt]\n    } else if (ref.length === alt.length) {\n      if (ref.split('').reverse().join('') === alt) {\n        return ['inversion', this._makeDescriptionString('inversion', ref, alt)]\n      }\n      return [\n        'substitution',\n        this._makeDescriptionString('substitution', ref, alt),\n      ]\n    } else if (ref.length <= alt.length) {\n      return ['insertion', this._makeDescriptionString('insertion', ref, alt)]\n    } else if (ref.length > alt.length) {\n      return ['deletion', this._makeDescriptionString('deletion', ref, alt)]\n    }\n\n    return ['indel', this._makeDescriptionString('indel', ref, alt)]\n  }\n\n  _makeDescriptionString(soTerm: string, ref: string, alt: string): string {\n    return `${soTerm} ${ref} -> ${alt}`\n  }\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  toJSON(): any {\n    return {\n      uniqueId: this._id,\n      ...this.variant,\n      ...this.data,\n      samples: this.variant.SAMPLES,\n    }\n  }\n}\n","import { lazy } from 'react'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\nimport {\n  createBaseTrackConfig,\n  createBaseTrackModel,\n} from '@jbrowse/core/pluggableElementTypes/models'\nimport TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'\nimport WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'\nimport Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'\nimport ChordVariantDisplay from './ChordVariantDisplay'\nimport {\n  configSchemaFactory as linearVariantDisplayConfigSchemaFactory,\n  modelFactory as linearVariantDisplayModelFactory,\n} from './LinearVariantDisplay'\nimport StructuralVariantChordRendererFactory from './StructuralVariantChordRenderer'\nimport {\n  configSchema as variantFeatureWidgetConfigSchema,\n  stateModelFactory as variantFeatureWidgetStateModelFactory,\n} from './VariantFeatureWidget'\nimport { configSchema as vcfTabixAdapterConfigSchema } from './VcfTabixAdapter'\nimport { configSchema as vcfAdapterConfigSchema } from './VcfAdapter'\n\nexport default class VariantsPlugin extends Plugin {\n  name = 'VariantsPlugin'\n\n  install(pluginManager: PluginManager) {\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'VcfTabixAdapter',\n          configSchema: vcfTabixAdapterConfigSchema,\n          getAdapterClass: () =>\n            import('./VcfTabixAdapter/VcfTabixAdapter').then(r => r.default),\n        }),\n    )\n\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'VcfAdapter',\n          configSchema: vcfAdapterConfigSchema,\n          getAdapterClass: () =>\n            import('./VcfAdapter/VcfAdapter').then(r => r.default),\n        }),\n    )\n\n    pluginManager.addRendererType(() =>\n      pluginManager.jbrequire(StructuralVariantChordRendererFactory),\n    )\n    pluginManager.addTrackType(() => {\n      const configSchema = ConfigurationSchema(\n        'VariantTrack',\n        {},\n        { baseConfiguration: createBaseTrackConfig(pluginManager) },\n      )\n      return new TrackType({\n        name: 'VariantTrack',\n        configSchema,\n        stateModel: createBaseTrackModel(\n          pluginManager,\n          'VariantTrack',\n          configSchema,\n        ),\n      })\n    })\n\n    pluginManager.addDisplayType(() =>\n      pluginManager.jbrequire(ChordVariantDisplay),\n    )\n\n    pluginManager.addDisplayType(() => {\n      const configSchema = linearVariantDisplayConfigSchemaFactory(\n        pluginManager,\n      )\n      return new DisplayType({\n        name: 'LinearVariantDisplay',\n        configSchema,\n        stateModel: linearVariantDisplayModelFactory(configSchema),\n        trackType: 'VariantTrack',\n        viewType: 'LinearGenomeView',\n        ReactComponent: BaseLinearDisplayComponent,\n      })\n    })\n\n    pluginManager.addWidgetType(\n      () =>\n        new WidgetType({\n          name: 'VariantFeatureWidget',\n          heading: 'Feature details',\n          configSchema: variantFeatureWidgetConfigSchema,\n          stateModel: variantFeatureWidgetStateModelFactory(pluginManager),\n          ReactComponent: lazy(\n            () => import('./VariantFeatureWidget/VariantFeatureWidget'),\n          ),\n        }),\n    )\n  }\n}\n\nexport { default as VcfFeature } from './VcfTabixAdapter/VcfFeature'\n","import {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport {\n  FileLocation,\n  NoAssemblyRegion,\n  Region,\n} from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { TabixIndexedFile } from '@gmod/tabix'\nimport { GenericFilehandle } from 'generic-filehandle'\nimport VcfParser from '@gmod/vcf'\nimport { Observer } from 'rxjs'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport VcfFeature from './VcfFeature'\n\nexport default class extends BaseFeatureDataAdapter {\n  protected configured?: Promise<{\n    vcf: TabixIndexedFile\n    parser: typeof VcfParser\n    filehandle: GenericFilehandle\n  }>\n\n  protected async configure() {\n    if (!this.configured) {\n      const vcfGzLocation = readConfObject(this.config, 'vcfGzLocation')\n      const location = readConfObject(this.config, ['index', 'location'])\n      const indexType = readConfObject(this.config, ['index', 'indexType'])\n\n      const filehandle = openLocation(vcfGzLocation as FileLocation)\n      const isCSI = indexType === 'CSI'\n      const vcf = new TabixIndexedFile({\n        filehandle,\n        csiFilehandle: isCSI ? openLocation(location) : undefined,\n        tbiFilehandle: !isCSI ? openLocation(location) : undefined,\n        chunkCacheSize: 50 * 2 ** 20,\n        chunkSizeLimit: 1000000000,\n      })\n\n      this.configured = vcf\n        .getHeader()\n        .then(header => ({\n          filehandle,\n          vcf,\n          parser: new VcfParser({ header }),\n        }))\n        .catch(e => {\n          this.configured = undefined\n          throw e\n        })\n    }\n    return this.configured\n  }\n\n  public async getRefNames(opts: BaseOptions = {}) {\n    const { vcf } = await this.configure()\n    return vcf.getReferenceSequenceNames(opts)\n  }\n\n  async getHeader() {\n    const { vcf } = await this.configure()\n    return vcf.getHeader()\n  }\n\n  async getMetadata() {\n    const { parser } = await this.configure()\n    return parser.getMetadata()\n  }\n\n  public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const { refName, start, end } = query\n      const { vcf, parser } = await this.configure()\n      await vcf.getLines(refName, start, end, {\n        lineCallback: (line: string, fileOffset: number) => {\n          observer.next(\n            new VcfFeature({\n              variant: parser.parseLine(line),\n              parser,\n              id: `${this.id}-vcf-${fileOffset}`,\n            }),\n          )\n        },\n        ...opts,\n      })\n      observer.complete()\n    }, opts.signal)\n  }\n\n  /**\n   * Checks if the data source has data for the given reference sequence,\n   * and then gets the features in the region if it does\n   *\n   * Currently this just calls getFeatureInRegion for each region. Adapters that\n   * are frequently called on multiple regions simultaneously may want to\n   * implement a more efficient custom version of this method.\n   *\n   * Also includes a bit of extra logging to warn when fetching a large portion\n   * of a VCF\n   * @param regions - Regions\n   * @param opts - Feature adapter options\n   * @returns Observable of Feature objects in the regions\n   */\n  public getFeaturesInMultipleRegions(\n    regions: Region[],\n    opts: BaseOptions = {},\n  ) {\n    // TODO: restore commented version below once TSDX supports Rollup v2\n    // xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45\n    const superGetFeaturesInMultipleRegions = super.getFeaturesInMultipleRegions\n    return ObservableCreate<Feature>(async (observer: Observer<Feature>) => {\n      const bytes = await this.bytesForRegions(regions)\n      const { filehandle } = await this.configure()\n      const stat = await filehandle.stat()\n      let pct = Math.round((bytes / stat.size) * 100)\n      if (pct > 100) {\n        // this is just a bad estimate, make 100% if it goes over\n        pct = 100\n      }\n      if (pct > 60) {\n        console.warn(\n          `getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`,\n        )\n      }\n      superGetFeaturesInMultipleRegions\n        .call(this, regions, opts)\n        .subscribe(observer)\n      // super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)\n    })\n  }\n\n  /**\n   * get the approximate number of bytes queried from the file for the given\n   * query regions\n   * @param regions - list of query regions\n   */\n  private async bytesForRegions(regions: Region[]) {\n    const { vcf } = await this.configure()\n    const blockResults = await Promise.all(\n      regions.map(region =>\n        // @ts-ignore\n        vcf.index.blocksForRange(region.refName, region.start, region.end),\n      ),\n    )\n    interface ByteRange {\n      start: number\n      end: number\n    }\n    interface VirtualOffset {\n      blockPosition: number\n    }\n    interface Block {\n      minv: VirtualOffset\n      maxv: VirtualOffset\n    }\n    const byteRanges: ByteRange[] = []\n    blockResults.forEach((blocks: Block[]) => {\n      blocks.forEach(block => {\n        const start = block.minv.blockPosition\n        const end = block.maxv.blockPosition + 64000\n        if (\n          !byteRanges.find(range => {\n            if (range.start <= end && range.end >= start) {\n              range.start = Math.min(range.start, start)\n              range.end = Math.max(range.end, end)\n              return true\n            }\n            return false\n          })\n        ) {\n          byteRanges.push({ start, end })\n        }\n      })\n    })\n\n    return byteRanges.reduce((a, b) => a + b.end - b.start + 1, 0)\n  }\n\n  public freeResources(/* { region } */): void {}\n}\n","import {\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 { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'\nimport VcfFeature from '../VcfTabixAdapter/VcfFeature'\nimport VCF from '@gmod/vcf'\nimport { unzip } from '@gmod/bgzf-filehandle'\n\nconst readVcf = (f: string) => {\n  const lines = f.split('\\n')\n  const header: string[] = []\n  const refNames: string[] = []\n  const rest: string[] = []\n  lines.forEach(line => {\n    if (line.startsWith('##contig')) {\n      refNames.push(line.split('##contig=<ID=')[1].split(',')[0])\n    } else if (line.startsWith('#')) {\n      header.push(line)\n    } else if (line) {\n      rest.push(line)\n    }\n  })\n  return { header: header.join('\\n'), lines: rest, refNames }\n}\n\nexport default class VcfAdapter extends BaseFeatureDataAdapter {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private setupP?: Promise<Feature[]>\n\n  public constructor(config: AnyConfigurationModel) {\n    super(config)\n  }\n\n  private async decodeFileContents() {\n    const vcfLocation = readConfObject(\n      this.config,\n      'vcfLocation',\n    ) as FileLocation\n\n    let fileContents = await openLocation(vcfLocation).readFile()\n\n    if (\n      typeof fileContents[0] === 'number' &&\n      fileContents[0] === 31 &&\n      typeof fileContents[1] === 'number' &&\n      fileContents[1] === 139 &&\n      typeof fileContents[2] === 'number' &&\n      fileContents[2] === 8\n    ) {\n      fileContents = new TextDecoder().decode(await unzip(fileContents))\n    } else {\n      fileContents = fileContents.toString()\n    }\n\n    return readVcf(fileContents)\n  }\n\n  public async getHeader() {\n    const { header } = await this.decodeFileContents()\n    return header\n  }\n\n  async getMetadata() {\n    const { header } = await this.decodeFileContents()\n    const parser = new VCF({ header: header })\n    return parser.getMetadata()\n  }\n\n  public async getLines() {\n    const { header, lines } = await this.decodeFileContents()\n\n    const parser = new VCF({ header: header })\n\n    return lines.map((line, index) => {\n      return new VcfFeature({\n        variant: parser.parseLine(line),\n        parser,\n        id: `${this.id}-vcf-${index}`,\n      })\n    })\n  }\n\n  public async setup() {\n    if (!this.setupP) {\n      this.setupP = this.getLines()\n    }\n    return this.setupP\n  }\n\n  public async getRefNames(_: BaseOptions = {}) {\n    const { refNames } = await this.decodeFileContents()\n    return refNames\n  }\n\n  public getFeatures(region: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const feats = await this.setup()\n      feats.forEach(f => {\n        if (\n          f.get('refName') === region.refName &&\n          f.get('end') > region.start &&\n          f.get('start') < region.end\n        ) {\n          observer.next(f)\n        }\n      })\n      observer.complete()\n    }, opts.signal)\n  }\n\n  public freeResources(): void {}\n}\n","/* eslint-disable @typescript-eslint/no-explicit-any */\nimport React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from '@material-ui/core/styles'\nimport {\n  Button,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogTitle,\n  Divider,\n  IconButton,\n  FormControlLabel,\n  Checkbox,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\nimport { getSnapshot } from 'mobx-state-tree'\nimport { getSession } from '@jbrowse/core/util'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\n\nconst useStyles = makeStyles(theme => ({\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n  block: {\n    display: 'block',\n  },\n}))\n\nfunction BreakendOptionDialog({\n  model,\n  handleClose,\n  feature,\n  viewType,\n}: {\n  model: any\n  handleClose: () => void\n  feature: Feature\n  viewType: any\n}) {\n  const classes = useStyles()\n  const [copyTracks, setCopyTracks] = useState(true)\n  const [mirrorTracks, setMirrorTracks] = useState(true)\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Breakpoint split view options\n        {handleClose ? (\n          <IconButton\n            className={classes.closeButton}\n            onClick={() => {\n              handleClose()\n            }}\n          >\n            <CloseIcon />\n          </IconButton>\n        ) : null}\n      </DialogTitle>\n      <Divider />\n\n      <DialogContent>\n        <FormControlLabel\n          className={classes.block}\n          control={\n            <Checkbox\n              checked={copyTracks}\n              onChange={() => setCopyTracks(val => !val)}\n            />\n          }\n          label=\"Copy tracks into the new view\"\n        />\n\n        <FormControlLabel\n          className={classes.block}\n          control={\n            <Checkbox\n              checked={mirrorTracks}\n              onChange={() => setMirrorTracks(val => !val)}\n            />\n          }\n          label=\"Mirror tracks vertically in vertically stacked view\"\n        />\n      </DialogContent>\n      <DialogActions>\n        <Button\n          onClick={() => {\n            const { view } = model\n            const session = getSession(model)\n\n            const viewSnapshot = viewType.snapshotFromBreakendFeature(\n              feature,\n              view,\n            )\n            viewSnapshot.views[0].offsetPx -= view.width / 2 + 100\n            viewSnapshot.views[1].offsetPx -= view.width / 2 + 100\n            viewSnapshot.featureData = feature\n            const viewTracks: any = getSnapshot(view.tracks)\n            viewSnapshot.views[0].tracks = viewTracks\n            viewSnapshot.views[1].tracks = mirrorTracks\n              ? viewTracks.slice().reverse()\n              : viewTracks\n\n            session.addView('BreakpointSplitView', viewSnapshot)\n\n            handleClose()\n          }}\n          variant=\"contained\"\n          color=\"primary\"\n          autoFocus\n        >\n          OK\n        </Button>\n        <Button\n          onClick={() => {\n            handleClose()\n          }}\n          color=\"secondary\"\n          variant=\"contained\"\n          autoFocus\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n}\nexport default observer(BreakendOptionDialog)\n","/* eslint-disable @typescript-eslint/no-explicit-any */\nimport React, { useState } from 'react'\nimport {\n  Divider,\n  Link,\n  Paper,\n  FormControlLabel,\n  Checkbox,\n  TextField,\n  Typography,\n} from '@material-ui/core'\nimport SimpleFeature, {\n  SimpleFeatureSerialized,\n} from '@jbrowse/core/util/simpleFeature'\nimport { DataGrid } from '@material-ui/data-grid'\nimport { observer } from 'mobx-react'\nimport { getSession } from '@jbrowse/core/util'\nimport { getEnv } from 'mobx-state-tree'\nimport {\n  FeatureDetails,\n  BaseCard,\n} from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'\nimport BreakendOptionDialog from './BreakendOptionDialog'\nimport { parseBreakend } from '@gmod/vcf'\n\nfunction VariantSamples(props: any) {\n  const [filter, setFilter] = useState<any>({})\n  const [showFilters, setShowFilters] = useState(false)\n  const { feature } = props\n\n  const { samples = {} } = feature\n  const preFilteredRows: any = Object.entries(samples)\n  if (!preFilteredRows.length) {\n    return null\n  }\n  const infoFields = ['sample', ...Object.keys(preFilteredRows[0][1])].map(\n    field => ({\n      field,\n    }),\n  )\n  let error\n  let rows = []\n  const filters = Object.keys(filter)\n\n  // catch some error thrown from regex\n  // note: maps all values into a string, if this is not done rows are not\n  // sortable by the data-grid\n  try {\n    rows = preFilteredRows\n      .map((row: any) => ({\n        ...Object.fromEntries(\n          Object.entries(row[1]).map(entry => [entry[0], String(entry[1])]),\n        ),\n        sample: row[0],\n        id: row[0],\n      }))\n      .filter((row: any) => {\n        return filters.length\n          ? filters.every(key => {\n              const val = row[key]\n              const currFilter = filter[key]\n              return currFilter ? val.match(new RegExp(currFilter, 'i')) : true\n            })\n          : true\n      })\n  } catch (e) {\n    error = e\n  }\n  // disableSelectionOnClick helps avoid\n  // https://github.com/mui-org/material-ui-x/issues/1197\n  return (\n    <BaseCard {...props} title=\"Samples\">\n      {error ? <Typography color=\"error\">{`${error}`}</Typography> : null}\n\n      <FormControlLabel\n        control={\n          <Checkbox\n            checked={showFilters}\n            onChange={() => setShowFilters(f => !f)}\n          />\n        }\n        label=\"Show sample filters\"\n      />\n      {showFilters ? (\n        <>\n          <Typography>\n            These filters can use a plain text search or regex style query, e.g.\n            in the genotype field, entering 1 will query for all genotypes that\n            include the first alternate allele e.g. 0|1 or 1|1, entering\n            [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33\n          </Typography>\n          {infoFields.map(({ field }) => {\n            return (\n              <TextField\n                key={`filter-${field}`}\n                placeholder={`Filter ${field}`}\n                value={filter[field] || ''}\n                onChange={event =>\n                  setFilter({ ...filter, [field]: event.target.value })\n                }\n              />\n            )\n          })}\n        </>\n      ) : null}\n      <div style={{ height: 600, width: '100%', overflow: 'auto' }}>\n        <DataGrid\n          rows={rows}\n          columns={infoFields}\n          rowHeight={20}\n          headerHeight={25}\n          disableSelectionOnClick\n          disableColumnMenu\n        />\n      </div>\n    </BaseCard>\n  )\n}\n\nfunction BreakendPanel(props: {\n  locStrings: string[]\n  model: any\n  feature: SimpleFeatureSerialized\n}) {\n  const { model, locStrings, feature } = props\n  const session = getSession(model)\n  const { pluginManager } = getEnv(session)\n  const [breakpointDialog, setBreakpointDialog] = useState(false)\n  let viewType\n\n  try {\n    viewType = pluginManager.getViewType('BreakpointSplitView')\n  } catch (e) {\n    // ignore\n  }\n\n  const simpleFeature = new SimpleFeature(feature)\n  return (\n    <BaseCard {...props} title=\"Breakends\">\n      <Typography>Link to linear view of breakend endpoints</Typography>\n      <ul>\n        {locStrings.map(locString => (\n          <li key={`${JSON.stringify(locString)}`}>\n            <Link\n              href=\"#\"\n              onClick={(event: any) => {\n                event.preventDefault()\n                const { view } = model\n                if (view) {\n                  view.navToLocString?.(locString)\n                } else {\n                  session.notify(\n                    'No view associated with this feature detail panel anymore',\n                    'warning',\n                  )\n                }\n              }}\n            >\n              {`LGV - ${locString}`}\n            </Link>\n          </li>\n        ))}\n      </ul>\n      {viewType ? (\n        <div>\n          <Typography>\n            Launch split views with breakend source and target\n          </Typography>\n          <ul>\n            {locStrings.map(locString => (\n              <li key={`${JSON.stringify(locString)}`}>\n                <Link\n                  href=\"#\"\n                  onClick={(event: any) => {\n                    event.preventDefault()\n                    setBreakpointDialog(true)\n                  }}\n                >\n                  {`${feature.refName}:${feature.start} // ${locString} (split view)`}\n                </Link>\n              </li>\n            ))}\n          </ul>\n          {breakpointDialog ? (\n            <BreakendOptionDialog\n              model={model}\n              feature={simpleFeature}\n              viewType={viewType}\n              handleClose={() => {\n                setBreakpointDialog(false)\n              }}\n            />\n          ) : null}\n        </div>\n      ) : null}\n    </BaseCard>\n  )\n}\n\nfunction VariantFeatureDetails(props: any) {\n  const { model } = props\n  const { featureData, descriptions } = model\n  const feat = JSON.parse(JSON.stringify(featureData))\n  const { samples, ...rest } = feat\n  const basicDescriptions = {\n    CHROM: 'chromosome: An identifier from the reference genome',\n    POS:\n      'position: The reference position, with the 1st base having position 1',\n    ID:\n      'identifier: Semi-colon separated list of unique identifiers where available',\n    REF:\n      'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',\n    ALT:\n      'alternate base(s): Comma-separated list of alternate non-reference alleles',\n    QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',\n    FILTER:\n      'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',\n  }\n\n  return (\n    <Paper data-testid=\"variant-side-drawer\">\n      <FeatureDetails\n        feature={rest}\n        descriptions={{ ...basicDescriptions, ...descriptions }}\n        {...props}\n      />\n      <Divider />\n      {feat.type === 'breakend' ? (\n        <BreakendPanel\n          feature={feat}\n          locStrings={feat.ALT.map(\n            (alt: string) => parseBreakend(alt).MatePosition,\n          )}\n          model={model}\n        />\n      ) : null}\n      {feat.type === 'translocation' ? (\n        <BreakendPanel\n          feature={feat}\n          model={model}\n          locStrings={[`${feat.INFO.CHR2[0]}:${feat.INFO.END}`]}\n        />\n      ) : null}\n      <VariantSamples feature={feat} {...props} />\n    </Paper>\n  )\n}\n\nexport default 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+{"version":3,"file":"plugin-variants.cjs.development.js","sources":["../src/ChordVariantDisplay/models/ChordVariantDisplay.js","../src/ChordVariantDisplay/index.ts","../src/LinearVariantDisplay/configSchema.ts","../../../node_modules/regenerator-runtime/runtime.js","../src/LinearVariantDisplay/model.ts","../src/StructuralVariantChordRenderer/ReactComponent.js","../src/StructuralVariantChordRenderer/index.js","../src/VariantFeatureWidget/index.js","../src/VcfTabixAdapter/configSchema.ts","../src/VcfAdapter/configSchema.ts","../src/VcfTabixAdapter/VcfFeature.ts","../src/index.ts","../src/VcfTabixAdapter/VcfTabixAdapter.ts","../src/VcfAdapter/VcfAdapter.ts","../src/VariantFeatureWidget/BreakendOptionDialog.tsx","../src/VariantFeatureWidget/VariantFeatureWidget.tsx"],"sourcesContent":["import {\n  baseChordDisplayConfig,\n  BaseChordDisplayModel,\n} from '@jbrowse/plugin-circular-view'\n\nconst ChordVariantDisplayF = pluginManager => {\n  const { jbrequire } = pluginManager\n\n  const { types } = jbrequire('mobx-state-tree')\n  const { ConfigurationSchema, ConfigurationReference } = jbrequire(\n    '@jbrowse/core/configuration',\n  )\n  const { getContainingView } = jbrequire('@jbrowse/core/util')\n  const { getParentRenderProps } = jbrequire('@jbrowse/core/util/tracks')\n  const configSchema = ConfigurationSchema(\n    'ChordVariantDisplay',\n    {\n      renderer: types.optional(\n        pluginManager.pluggableConfigSchemaType('renderer'),\n        { type: 'StructuralVariantChordRenderer' },\n      ),\n    },\n    { baseConfiguration: baseChordDisplayConfig, explicitlyTyped: true },\n  )\n\n  const stateModel = types\n    .compose(\n      'ChordVariantDisplay',\n      BaseChordDisplayModel,\n      types.model({\n        type: types.literal('ChordVariantDisplay'),\n        configuration: ConfigurationReference(configSchema),\n      }),\n    )\n    .views(self => ({\n      get rendererTypeName() {\n        return self.configuration.renderer.type\n      },\n\n      renderProps() {\n        const view = getContainingView(self)\n        return {\n          ...getParentRenderProps(self),\n          rpcDriverName: self.rpcDriverName,\n          displayModel: self,\n          bezierRadius: view.radiusPx * self.bezierRadiusRatio,\n          radius: view.radiusPx,\n          blockDefinitions: this.blockDefinitions,\n          config: self.configuration.renderer,\n          onChordClick: self.onChordClick,\n        }\n      },\n    }))\n\n  return { stateModel, configSchema }\n}\n\n// http://localhost:3000/test_data/hs37d5.HG002-SequelII-CCS.sv.vcf.gz.tbi\n\n// render request is for 1.5x the current viewing window\n\n// tracks all have a height\n//\nexport default ChordVariantDisplayF\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport { BaseChordDisplayComponentFactory } from '@jbrowse/plugin-circular-view'\nimport ChordVariantDisplay from './models/ChordVariantDisplay'\n\nexport default (pluginManager: PluginManager) => {\n  const { lib, load } = pluginManager\n  const DisplayType = lib['@jbrowse/core/pluggableElementTypes/DisplayType']\n\n  const { stateModel, configSchema } = load(ChordVariantDisplay)\n\n  return new DisplayType({\n    name: 'ChordVariantDisplay',\n    configSchema,\n    stateModel,\n    trackType: 'VariantTrack',\n    viewType: 'CircularView',\n    ReactComponent: BaseChordDisplayComponentFactory(pluginManager),\n  })\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { Instance } from 'mobx-state-tree'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view'\n\nexport function LinearVariantDisplayConfigFactory(\n  pluginManager: PluginManager,\n) {\n  const configSchema = linearBasicDisplayConfigSchemaFactory(pluginManager)\n\n  return ConfigurationSchema(\n    'LinearVariantDisplay',\n    {},\n    { baseConfiguration: configSchema, explicitlyTyped: true },\n  )\n}\n\nexport type LinearVariantDisplayConfigModel = ReturnType<\n  typeof LinearVariantDisplayConfigFactory\n>\nexport type LinearVariantDisplayConfig =\n  Instance<LinearVariantDisplayConfigModel>\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 { getConf, ConfigurationReference } from '@jbrowse/core/configuration'\nimport { getRpcSessionId } from '@jbrowse/core/util/tracks'\nimport {\n  getContainingTrack,\n  getSession,\n  getContainingView,\n  isSessionModelWithWidgets,\n} from '@jbrowse/core/util'\n\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { linearBasicDisplayModelFactory } from '@jbrowse/plugin-linear-genome-view'\nimport { types } from 'mobx-state-tree'\nimport { LinearVariantDisplayConfigModel } from './configSchema'\n\nexport default function (configSchema: LinearVariantDisplayConfigModel) {\n  return types\n    .compose(\n      'LinearVariantDisplay',\n      linearBasicDisplayModelFactory(configSchema),\n      types.model({\n        type: types.literal('LinearVariantDisplay'),\n        configuration: ConfigurationReference(configSchema),\n      }),\n    )\n    .actions(self => ({\n      async selectFeature(feature: Feature) {\n        const session = getSession(self)\n        if (isSessionModelWithWidgets(session)) {\n          const { rpcManager } = session\n          const sessionId = getRpcSessionId(self)\n          const track = getContainingTrack(self)\n          const adapterConfig = getConf(track, 'adapter')\n          const header = await rpcManager.call(sessionId, 'CoreGetMetadata', {\n            adapterConfig,\n          })\n          const featureWidget = session.addWidget(\n            'VariantFeatureWidget',\n            'variantFeature',\n            {\n              featureData: feature.toJSON(),\n              view: getContainingView(self),\n              descriptions: header,\n            },\n          )\n          session.showWidget(featureWidget)\n        }\n\n        session.setSelection(feature)\n      },\n    }))\n}\n","import React, { useMemo } from 'react'\nimport { observer, PropTypes as MobxPropTypes } from 'mobx-react'\nimport { polarToCartesian } from '@jbrowse/core/util'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { PropTypes as CommonPropTypes } from '@jbrowse/core/util/types/mst'\nimport { parseBreakend } from '@gmod/vcf'\nimport PropTypes from 'prop-types'\n\nfunction bpToRadians(block, pos) {\n  const blockStart = block.region.elided ? 0 : block.region.start\n  const blockEnd = block.region.elided ? 0 : block.region.end\n  const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart\n  const radians = bpOffset / block.bpPerRadian + block.startRadians\n  return radians\n}\n\nconst Chord = observer(function Chord({\n  feature,\n  blocksForRefs,\n  radius,\n  config,\n  bezierRadius,\n  selected,\n  onClick,\n}) {\n  // find the blocks that our start and end points belong to\n  const startBlock = blocksForRefs[feature.get('refName')]\n  if (!startBlock) {\n    return null\n  }\n  let svType\n  if (feature.get('INFO')) {\n    ;[svType] = feature.get('INFO').SVTYPE || []\n  } else if (feature.get('mate')) {\n    svType = 'mate'\n  }\n  let endPosition\n  let endBlock\n  const alt = feature.get('ALT')?.[0]\n  const bnd = alt && parseBreakend(alt)\n  if (bnd) {\n    // VCF BND\n    const matePosition = bnd.MatePosition.split(':')\n    endPosition = +matePosition[1]\n    endBlock = blocksForRefs[matePosition[0]]\n  } else if (alt === '<TRA>') {\n    // VCF TRA\n    const chr2 = feature.get('INFO')?.CHR2?.[0]\n    const end = feature.get('INFO')?.END?.[0]\n    endPosition = parseInt(end, 10)\n    endBlock = blocksForRefs[chr2]\n  } else if (svType === 'mate') {\n    // generic simplefeatures arcs\n    const mate = feature.get('mate')\n    const chr2 = mate.refName\n    endPosition = mate.start\n    endBlock = blocksForRefs[chr2]\n  }\n\n  if (endBlock) {\n    const startPos = feature.get('start')\n    const startRadians = bpToRadians(startBlock, startPos)\n    const endRadians = bpToRadians(endBlock, endPosition)\n    const startXY = polarToCartesian(radius, startRadians)\n    const endXY = polarToCartesian(radius, endRadians)\n    const controlXY = polarToCartesian(\n      bezierRadius,\n      (endRadians + startRadians) / 2,\n    )\n\n    const strokeColor = selected\n      ? readConfObject(config, 'strokeColorSelected', { feature })\n      : readConfObject(config, 'strokeColor', { feature })\n\n    const hoverStrokeColor = readConfObject(config, 'strokeColorHover', {\n      feature,\n    })\n    return (\n      <path\n        data-testid={`chord-${feature.id()}`}\n        d={['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' ')}\n        style={{ stroke: strokeColor }}\n        onClick={evt =>\n          onClick(feature, startBlock.region, endBlock.region, evt)\n        }\n        onMouseOver={evt => {\n          if (!selected) {\n            evt.target.style.stroke = hoverStrokeColor\n            evt.target.style.strokeWidth = 3\n          }\n        }}\n        onMouseOut={evt => {\n          if (!selected) {\n            evt.target.style.stroke = strokeColor\n            evt.target.style.strokeWidth = 1\n          }\n        }}\n      />\n    )\n  }\n\n  return null\n})\n\nfunction StructuralVariantChords(props) {\n  const {\n    features,\n    config,\n    displayModel,\n    blockDefinitions,\n    radius,\n    bezierRadius,\n    displayModel: { selectedFeatureId },\n\n    onChordClick,\n  } = props\n  // make a map of refName -> blockDefinition\n  const blocksForRefsMemo = useMemo(() => {\n    const blocksForRefs = {}\n    blockDefinitions.forEach(block => {\n      const regions = block.region.elided\n        ? block.region.regions\n        : [block.region]\n      regions.forEach(region => {\n        blocksForRefs[region.refName] = block\n      })\n    })\n    return blocksForRefs\n  }, [blockDefinitions])\n  // console.log(blocksForRefs)\n  const chords = []\n  for (const [id, feature] of features) {\n    const selected = String(selectedFeatureId) === String(feature.id())\n    chords.push(\n      <Chord\n        key={id}\n        feature={feature}\n        config={config}\n        displayModel={displayModel}\n        radius={radius}\n        bezierRadius={bezierRadius}\n        blocksForRefs={blocksForRefsMemo}\n        selected={selected}\n        onClick={onChordClick}\n      />,\n    )\n  }\n  const trackStyleId = `chords-${displayModel.id}`\n  return (\n    <g id={trackStyleId} data-testid=\"structuralVariantChordRenderer\">\n      <style\n        // eslint-disable-next-line react/no-danger\n        dangerouslySetInnerHTML={{\n          __html: `\n          #${trackStyleId} > path {\n            cursor: crosshair;\n            fill: none;\n          }\n`,\n        }}\n      />\n      {chords}\n    </g>\n  )\n}\n\nStructuralVariantChords.propTypes = {\n  features: PropTypes.instanceOf(Map).isRequired,\n  config: CommonPropTypes.ConfigSchema.isRequired,\n  displayModel: MobxPropTypes.objectOrObservableObject,\n  blockDefinitions: PropTypes.arrayOf(MobxPropTypes.objectOrObservableObject)\n    .isRequired,\n  radius: PropTypes.number.isRequired,\n  bezierRadius: PropTypes.number.isRequired,\n  selectedFeatureId: PropTypes.string,\n  onChordClick: PropTypes.oneOfType([PropTypes.func, PropTypes.string]),\n}\n\nStructuralVariantChords.defaultProps = {\n  displayModel: undefined,\n  selectedFeatureId: '',\n  onChordClick: undefined,\n}\n\nexport default observer(StructuralVariantChords)\n","import ChordRendererType from '@jbrowse/core/pluggableElementTypes/renderers/CircularChordRendererType'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport ReactComponent from './ReactComponent'\n\nconst ChordRendererConfigF = pluginManager => {\n  const configSchema = ConfigurationSchema(\n    'StructuralVariantChordRenderer',\n    {\n      strokeColor: {\n        type: 'color',\n        description: 'the line color of each arc',\n        defaultValue: 'rgba(255,133,0,0.32)',\n        contextVariable: ['feature'],\n      },\n      strokeColorSelected: {\n        type: 'color',\n        description: 'the line color of an arc that has been selected',\n        defaultValue: 'black',\n        contextVariable: ['feature'],\n      },\n      strokeColorHover: {\n        type: 'color',\n        description:\n          'the line color of an arc that is being hovered over with the mouse',\n        defaultValue: '#555',\n        contextVariable: ['feature'],\n      },\n    },\n    { explicitlyTyped: true },\n  )\n  return new ChordRendererType({\n    name: 'StructuralVariantChordRenderer',\n    ReactComponent,\n    configSchema,\n    pluginManager,\n  })\n}\n\nexport default ChordRendererConfigF\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { ElementId } from '@jbrowse/core/util/types/mst'\nimport { types } from 'mobx-state-tree'\n\nexport const configSchema = ConfigurationSchema('VariantFeatureWidget', {})\n\nexport function stateModelFactory(pluginManager) {\n  return types\n    .model('VariantFeatureWidget', {\n      id: ElementId,\n      type: types.literal('VariantFeatureWidget'),\n      view: types.safeReference(\n        pluginManager.pluggableMstType('view', 'stateModel'),\n      ),\n      featureData: types.frozen(),\n      descriptions: types.frozen(),\n    })\n    .actions(self => ({\n      setFeatureData(data) {\n        self.featureData = data\n      },\n      clearFeatureData() {\n        self.featureData = undefined\n      },\n    }))\n}\n","import { types } from 'mobx-state-tree'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'VcfTabixAdapter',\n  {\n    vcfGzLocation: {\n      type: 'fileLocation',\n      defaultValue: { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' },\n    },\n    index: ConfigurationSchema('VcfIndex', {\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.vcf.gz.tbi',\n          locationType: 'UriLocation',\n        },\n      },\n    }),\n  },\n  { explicitlyTyped: true },\n)\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'VcfAdapter',\n  {\n    vcfLocation: {\n      type: 'fileLocation',\n      defaultValue: { uri: '/path/to/my.vcf', locationType: 'UriLocation' },\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { parseBreakend } from '@gmod/vcf'\n\n/* eslint-disable no-underscore-dangle */\n\n/**\n * VCF Feature creation with lazy genotype evaluation.\n */\ninterface Samples {\n  [key: string]: {\n    [key: string]: { values: string[] | number[] | null }\n  }\n}\n\ninterface FeatureData {\n  [key: string]: unknown\n  refName: string\n  start: number\n  end: number\n  description?: string\n  type?: string\n  name?: string\n  aliases?: string[]\n  samples?: Samples\n}\n\nexport default class VCFFeature implements Feature {\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  private variant: any\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  private parser: any\n\n  private data: FeatureData\n\n  private _id: string\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  constructor(args: { variant: any; parser: any; id: string }) {\n    this.variant = args.variant\n    this.parser = args.parser\n    this.data = this.dataFromVariant(this.variant)\n    this._id = args.id\n  }\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  get(field: string): any {\n    return field === 'samples'\n      ? this.variant.SAMPLES\n      : this.data[field] || this.variant[field]\n  }\n\n  set(): void {}\n\n  parent(): undefined {\n    return undefined\n  }\n\n  children(): undefined {\n    return undefined\n  }\n\n  tags(): string[] {\n    const t = [\n      ...Object.keys(this.data),\n      ...Object.keys(this.variant),\n      'samples',\n    ]\n    return t\n  }\n\n  id(): string {\n    return this._id\n  }\n\n  dataFromVariant(variant: {\n    REF: string\n    POS: number\n    ALT: string[]\n    CHROM: string\n    INFO: any // eslint-disable-line @typescript-eslint/no-explicit-any\n    ID: string[]\n  }): FeatureData {\n    const { REF, ALT, POS, CHROM, INFO, ID } = variant\n    const start = POS - 1\n    const [SO_term, description] = this._getSOTermAndDescription(REF, ALT)\n    const isTRA = ALT?.some(f => f === '<TRA>')\n    const isSymbolic = ALT?.some(f => f.indexOf('<') !== -1)\n\n    return {\n      refName: CHROM,\n      start,\n      end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,\n      description,\n      type: SO_term,\n      name: ID?.join(','),\n      aliases: ID && ID.length > 1 ? variant.ID.slice(1) : undefined,\n    }\n  }\n\n  /**\n   * Get a sequence ontology (SO) term that describes the variant type\n   */\n  _getSOTermAndDescription(\n    ref: string,\n    alt: string[],\n  ): [string, string] | [undefined, undefined] {\n    // it's just a remark if there are no alternate alleles\n    if (!alt || alt === []) {\n      return ['remark', 'no alternative alleles']\n    }\n\n    const soTerms = new Set<string>()\n    let descriptions = new Set<string>()\n    alt.forEach(a => {\n      let [soTerm, description] = this._getSOAndDescFromAltDefs(ref, a)\n\n      if (!soTerm) {\n        ;[soTerm, description] = this._getSOAndDescByExamination(ref, a)\n      }\n      if (soTerm && description) {\n        soTerms.add(soTerm)\n        descriptions.add(description)\n      }\n    })\n\n    // Combine descriptions like [\"SNV G -> A\", \"SNV G -> T\"] to [\"SNV G -> A,T\"]\n    if (descriptions.size > 1) {\n      const prefixes = new Set(\n        [...descriptions].map(desc => {\n          const prefix = desc.split('->')\n          return prefix[1] ? prefix[0] : desc\n        }),\n      )\n\n      const new_descs = [...prefixes].map(prefix => {\n        const suffixes = [...descriptions]\n          .map(desc => {\n            const pref = desc.split('-> ')\n            return pref[1] && pref[0] === prefix ? pref[1] : ''\n          })\n          .filter(f => !!f)\n\n        return suffixes.length\n          ? prefix + '-> ' + suffixes.join(',')\n          : [...descriptions].join(',')\n      })\n\n      descriptions = new Set(new_descs)\n    }\n    if (soTerms.size) {\n      return [[...soTerms].join(','), [...descriptions].join(',')]\n    }\n    return [undefined, undefined]\n  }\n\n  static _altTypeToSO: { [key: string]: string | undefined } = {\n    DEL: 'deletion',\n    INS: 'insertion',\n    DUP: 'duplication',\n    INV: 'inversion',\n    INVDUP: 'inverted duplication',\n    CNV: 'copy_number_variation',\n    TRA: 'translocation',\n    'DUP:TANDEM': 'tandem_duplication',\n    NON_REF: 'sequence_variant',\n    '*': 'sequence_variant',\n  }\n\n  _getSOAndDescFromAltDefs(\n    ref: string,\n    alt: string,\n  ): [string, string] | [undefined, undefined] {\n    if (typeof alt === 'string' && !alt.startsWith('<')) {\n      return [undefined, undefined]\n    }\n\n    // look for a definition with an SO type for this\n    let soTerm = VCFFeature._altTypeToSO[alt]\n    // if no SO term but ALT is in metadata, assume sequence_variant\n    if (!soTerm && this.parser.getMetadata('ALT', alt)) {\n      soTerm = 'sequence_variant'\n    }\n    if (soTerm) {\n      return [soTerm, alt]\n    }\n\n    // try to look for a definition for a parent term if we can\n    const modAlt = alt.split(':')\n    if (modAlt.length > 1) {\n      return this._getSOAndDescFromAltDefs(\n        ref,\n        `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`,\n      )\n    }\n\n    // no parent\n    return [undefined, undefined]\n  }\n\n  // note: term SNV is used instead of SNP because SO definition of SNP says\n  // abundance must be at least 1% in population, and can't be sure we meet\n  // that\n  _getSOAndDescByExamination(ref: string, alt: string): [string, string] {\n    const bnd = parseBreakend(alt)\n    if (bnd) {\n      return ['breakend', alt]\n    } else if (ref.length === 1 && alt.length === 1) {\n      return ['SNV', this._makeDescriptionString('SNV', ref, alt)]\n    } else if (alt === '<INS>') {\n      return ['insertion', alt]\n    } else if (alt === '<DEL>') {\n      return ['deletion', alt]\n    } else if (alt === '<INV>') {\n      return ['deletion', alt]\n    } else if (alt === '<TRA>') {\n      return ['translocation', alt]\n    } else if (alt.includes('<')) {\n      return ['sv', alt]\n    } else if (ref.length === alt.length) {\n      if (ref.split('').reverse().join('') === alt) {\n        return ['inversion', this._makeDescriptionString('inversion', ref, alt)]\n      }\n      return [\n        'substitution',\n        this._makeDescriptionString('substitution', ref, alt),\n      ]\n    } else if (ref.length <= alt.length) {\n      return ['insertion', this._makeDescriptionString('insertion', ref, alt)]\n    } else if (ref.length > alt.length) {\n      return ['deletion', this._makeDescriptionString('deletion', ref, alt)]\n    }\n\n    return ['indel', this._makeDescriptionString('indel', ref, alt)]\n  }\n\n  _makeDescriptionString(soTerm: string, ref: string, alt: string): string {\n    return `${soTerm} ${ref} -> ${alt}`\n  }\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  toJSON(): any {\n    return {\n      uniqueId: this._id,\n      ...this.variant,\n      ...this.data,\n      samples: this.variant.SAMPLES,\n    }\n  }\n}\n","import { lazy } from 'react'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\nimport {\n  createBaseTrackConfig,\n  createBaseTrackModel,\n} from '@jbrowse/core/pluggableElementTypes/models'\nimport { FileLocation } from '@jbrowse/core/util/types'\nimport TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'\nimport WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'\nimport Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'\nimport ChordVariantDisplay from './ChordVariantDisplay'\nimport {\n  configSchemaFactory as linearVariantDisplayConfigSchemaFactory,\n  modelFactory as linearVariantDisplayModelFactory,\n} from './LinearVariantDisplay'\nimport StructuralVariantChordRendererFactory from './StructuralVariantChordRenderer'\nimport {\n  configSchema as variantFeatureWidgetConfigSchema,\n  stateModelFactory as variantFeatureWidgetStateModelFactory,\n} from './VariantFeatureWidget'\nimport { configSchema as vcfTabixAdapterConfigSchema } from './VcfTabixAdapter'\nimport { configSchema as vcfAdapterConfigSchema } from './VcfAdapter'\nimport {\n  makeIndex,\n  makeIndexType,\n  AdapterGuesser,\n  getFileName,\n  TrackTypeGuesser,\n} from '@jbrowse/core/util/tracks'\n\nexport default class VariantsPlugin extends Plugin {\n  name = 'VariantsPlugin'\n\n  install(pluginManager: PluginManager) {\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'VcfTabixAdapter',\n          configSchema: vcfTabixAdapterConfigSchema,\n          getAdapterClass: () =>\n            import('./VcfTabixAdapter/VcfTabixAdapter').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 = /\\.vcf\\.b?gz$/i\n          const adapterName = 'VcfTabixAdapter'\n          const fileName = getFileName(file)\n          const indexName = index && getFileName(index)\n          if (regexGuess.test(fileName) || adapterHint === adapterName) {\n            return {\n              type: adapterName,\n              vcfGzLocation: 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    pluginManager.addToExtensionPoint(\n      'Core-guessTrackTypeForLocation',\n      (trackTypeGuesser: TrackTypeGuesser) => {\n        return (adapterName: string) => {\n          if (adapterName === 'VcfTabixAdapter') {\n            return 'VariantTrack'\n          }\n          return trackTypeGuesser(adapterName)\n        }\n      },\n    )\n\n    pluginManager.addAdapterType(\n      () =>\n        new AdapterType({\n          name: 'VcfAdapter',\n          configSchema: vcfAdapterConfigSchema,\n          getAdapterClass: () =>\n            import('./VcfAdapter/VcfAdapter').then(r => r.default),\n        }),\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 = /\\.vcf$/i\n          const adapterName = 'VcfAdapter'\n          const fileName = getFileName(file)\n          if (regexGuess.test(fileName) || adapterHint === adapterName) {\n            return {\n              type: adapterName,\n              vcfLocation: file,\n            }\n          }\n          return adapterGuesser(file, index, adapterHint)\n        }\n      },\n    )\n\n    pluginManager.addRendererType(() =>\n      pluginManager.jbrequire(StructuralVariantChordRendererFactory),\n    )\n    pluginManager.addTrackType(() => {\n      const configSchema = ConfigurationSchema(\n        'VariantTrack',\n        {},\n        { baseConfiguration: createBaseTrackConfig(pluginManager) },\n      )\n      return new TrackType({\n        name: 'VariantTrack',\n        configSchema,\n        stateModel: createBaseTrackModel(\n          pluginManager,\n          'VariantTrack',\n          configSchema,\n        ),\n      })\n    })\n\n    pluginManager.addDisplayType(() =>\n      pluginManager.jbrequire(ChordVariantDisplay),\n    )\n\n    pluginManager.addDisplayType(() => {\n      const configSchema =\n        linearVariantDisplayConfigSchemaFactory(pluginManager)\n      return new DisplayType({\n        name: 'LinearVariantDisplay',\n        configSchema,\n        stateModel: linearVariantDisplayModelFactory(configSchema),\n        trackType: 'VariantTrack',\n        viewType: 'LinearGenomeView',\n        ReactComponent: BaseLinearDisplayComponent,\n      })\n    })\n\n    pluginManager.addWidgetType(\n      () =>\n        new WidgetType({\n          name: 'VariantFeatureWidget',\n          heading: 'Feature details',\n          configSchema: variantFeatureWidgetConfigSchema,\n          stateModel: variantFeatureWidgetStateModelFactory(pluginManager),\n          ReactComponent: lazy(\n            () => import('./VariantFeatureWidget/VariantFeatureWidget'),\n          ),\n        }),\n    )\n  }\n}\n\nexport { default as VcfFeature } from './VcfTabixAdapter/VcfFeature'\n","import {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport {\n  FileLocation,\n  NoAssemblyRegion,\n  Region,\n} from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { TabixIndexedFile } from '@gmod/tabix'\nimport { GenericFilehandle } from 'generic-filehandle'\nimport VcfParser from '@gmod/vcf'\nimport { Observer } from 'rxjs'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport VcfFeature from './VcfFeature'\n\nexport default class extends BaseFeatureDataAdapter {\n  protected configured?: Promise<{\n    vcf: TabixIndexedFile\n    parser: typeof VcfParser\n    filehandle: GenericFilehandle\n  }>\n\n  protected async configure() {\n    if (!this.configured) {\n      const vcfGzLocation = readConfObject(this.config, 'vcfGzLocation')\n      const location = readConfObject(this.config, ['index', 'location'])\n      const indexType = readConfObject(this.config, ['index', 'indexType'])\n\n      const filehandle = openLocation(\n        vcfGzLocation as FileLocation,\n        this.pluginManager,\n      )\n      const isCSI = indexType === 'CSI'\n      const vcf = new TabixIndexedFile({\n        filehandle,\n        csiFilehandle: isCSI\n          ? openLocation(location, this.pluginManager)\n          : undefined,\n        tbiFilehandle: !isCSI\n          ? openLocation(location, this.pluginManager)\n          : undefined,\n        chunkCacheSize: 50 * 2 ** 20,\n        chunkSizeLimit: 1000000000,\n      })\n\n      this.configured = vcf\n        .getHeader()\n        .then(header => ({\n          filehandle,\n          vcf,\n          parser: new VcfParser({ header }),\n        }))\n        .catch(e => {\n          this.configured = undefined\n          throw e\n        })\n    }\n    return this.configured\n  }\n\n  public async getRefNames(opts: BaseOptions = {}) {\n    const { vcf } = await this.configure()\n    return vcf.getReferenceSequenceNames(opts)\n  }\n\n  async getHeader() {\n    const { vcf } = await this.configure()\n    return vcf.getHeader()\n  }\n\n  async getMetadata() {\n    const { parser } = await this.configure()\n    return parser.getMetadata()\n  }\n\n  public getFeatures(query: NoAssemblyRegion, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const { refName, start, end } = query\n      const { vcf, parser } = await this.configure()\n      await vcf.getLines(refName, start, end, {\n        lineCallback: (line: string, fileOffset: number) => {\n          observer.next(\n            new VcfFeature({\n              variant: parser.parseLine(line),\n              parser,\n              id: `${this.id}-vcf-${fileOffset}`,\n            }),\n          )\n        },\n        ...opts,\n      })\n      observer.complete()\n    }, opts.signal)\n  }\n\n  /**\n   * Checks if the data source has data for the given reference sequence,\n   * and then gets the features in the region if it does\n   *\n   * Currently this just calls getFeatureInRegion for each region. Adapters that\n   * are frequently called on multiple regions simultaneously may want to\n   * implement a more efficient custom version of this method.\n   *\n   * Also includes a bit of extra logging to warn when fetching a large portion\n   * of a VCF\n   * @param regions - Regions\n   * @param opts - Feature adapter options\n   * @returns Observable of Feature objects in the regions\n   */\n  public getFeaturesInMultipleRegions(\n    regions: Region[],\n    opts: BaseOptions = {},\n  ) {\n    // TODO: restore commented version below once TSDX supports Rollup v2\n    // xref: https://github.com/rollup/rollup/blob/master/CHANGELOG.md#bug-fixes-45\n    const superGetFeaturesInMultipleRegions = super.getFeaturesInMultipleRegions\n    return ObservableCreate<Feature>(async (observer: Observer<Feature>) => {\n      const bytes = await this.bytesForRegions(regions)\n      const { filehandle } = await this.configure()\n      const stat = await filehandle.stat()\n      let pct = Math.round((bytes / stat.size) * 100)\n      if (pct > 100) {\n        // this is just a bad estimate, make 100% if it goes over\n        pct = 100\n      }\n      if (pct > 60) {\n        console.warn(\n          `getFeaturesInMultipleRegions fetching ${pct}% of VCF file, but whole-file streaming not yet implemented`,\n        )\n      }\n      superGetFeaturesInMultipleRegions\n        .call(this, regions, opts)\n        .subscribe(observer)\n      // super.getFeaturesInMultipleRegions(regions, opts).subscribe(observer)\n    })\n  }\n\n  /**\n   * get the approximate number of bytes queried from the file for the given\n   * query regions\n   * @param regions - list of query regions\n   */\n  private async bytesForRegions(regions: Region[]) {\n    const { vcf } = await this.configure()\n    const blockResults = await Promise.all(\n      regions.map(region =>\n        // @ts-ignore\n        vcf.index.blocksForRange(region.refName, region.start, region.end),\n      ),\n    )\n    interface ByteRange {\n      start: number\n      end: number\n    }\n    interface VirtualOffset {\n      blockPosition: number\n    }\n    interface Block {\n      minv: VirtualOffset\n      maxv: VirtualOffset\n    }\n    const byteRanges: ByteRange[] = []\n    blockResults.forEach((blocks: Block[]) => {\n      blocks.forEach(block => {\n        const start = block.minv.blockPosition\n        const end = block.maxv.blockPosition + 64000\n        if (\n          !byteRanges.find(range => {\n            if (range.start <= end && range.end >= start) {\n              range.start = Math.min(range.start, start)\n              range.end = Math.max(range.end, end)\n              return true\n            }\n            return false\n          })\n        ) {\n          byteRanges.push({ start, end })\n        }\n      })\n    })\n\n    return byteRanges.reduce((a, b) => a + b.end - b.start + 1, 0)\n  }\n\n  public freeResources(/* { region } */): void {}\n}\n","import {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { Region } from '@jbrowse/core/util/types'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport IntervalTree from '@flatten-js/interval-tree'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport VCF from '@gmod/vcf'\nimport VcfFeature from '../VcfTabixAdapter/VcfFeature'\n\nconst readVcf = (f: string) => {\n  const lines = f.split('\\n')\n  const header: string[] = []\n  const rest: string[] = []\n  lines.forEach(line => {\n    if (line.startsWith('#')) {\n      header.push(line)\n    } else if (line) {\n      rest.push(line)\n    }\n  })\n  return { header: header.join('\\n'), lines: rest }\n}\n\nfunction isGzip(buf: Buffer) {\n  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8\n}\n\nexport default class VcfAdapter extends BaseFeatureDataAdapter {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  protected vcfFeatures?: Promise<{\n    header: string\n    intervalTree: Record<string, IntervalTree>\n  }>\n\n  public async getHeader() {\n    const { header } = await this.setup()\n    return header\n  }\n\n  async getMetadata() {\n    const { header } = await this.setup()\n    const parser = new VCF({ header: header })\n    return parser.getMetadata()\n  }\n\n  // converts lines into an interval tree\n  public async setupP() {\n    const buffer = await openLocation(\n      readConfObject(this.config, 'vcfLocation'),\n      this.pluginManager,\n    ).readFile()\n\n    const buf = isGzip(buffer as Buffer) ? await unzip(buffer) : buffer\n\n    // 512MB  max chrome string length is 512MB\n    if (buf.length > 536_870_888) {\n      throw new Error('Data exceeds maximum string length (512MB)')\n    }\n\n    const str = new TextDecoder().decode(buf)\n    const { header, lines } = readVcf(str)\n\n    const intervalTree = lines\n      .map((line, id) => {\n        const [refName, startP, , ref, , , , info] = line.split('\\t')\n        const start = +startP - 1\n        const end = +(info.match(/END=(\\d+)/)?.[1].trim() || start + ref.length)\n        return { line, refName, start, end, id }\n      })\n      .reduce((acc, obj) => {\n        const key = obj.refName\n        if (!acc[key]) {\n          acc[key] = new IntervalTree()\n        }\n        acc[key].insert([obj.start, obj.end], obj)\n        return acc\n      }, {} as Record<string, IntervalTree>)\n\n    return { header, intervalTree }\n  }\n\n  public async setup() {\n    if (!this.vcfFeatures) {\n      this.vcfFeatures = this.setupP().catch(e => {\n        this.vcfFeatures = undefined\n        throw e\n      })\n    }\n    return this.vcfFeatures\n  }\n\n  public async getRefNames(_: BaseOptions = {}) {\n    const { intervalTree } = await this.setup()\n    return Object.keys(intervalTree)\n  }\n\n  public getFeatures(region: Region, opts: BaseOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      try {\n        const { start, end, refName } = region\n        const { header, intervalTree } = await this.setup()\n        const parser = new VCF({ header: header })\n        intervalTree[refName]?.search([start, end]).forEach(f =>\n          observer.next(\n            new VcfFeature({\n              variant: parser.parseLine(f.line),\n              parser,\n              id: `${this.id}-${f.id}`,\n            }),\n          ),\n        )\n        observer.complete()\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 React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from '@material-ui/core/styles'\nimport {\n  Button,\n  Dialog,\n  DialogActions,\n  DialogContent,\n  DialogTitle,\n  Divider,\n  IconButton,\n  FormControlLabel,\n  Checkbox,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\nimport { getSnapshot } from 'mobx-state-tree'\nimport { getSession } from '@jbrowse/core/util'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\n\nconst useStyles = makeStyles(theme => ({\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n  block: {\n    display: 'block',\n  },\n}))\n\nfunction BreakendOptionDialog({\n  model,\n  handleClose,\n  feature,\n  viewType,\n}: {\n  model: any\n  handleClose: () => void\n  feature: Feature\n  viewType: any\n}) {\n  const classes = useStyles()\n  const [copyTracks, setCopyTracks] = useState(true)\n  const [mirrorTracks, setMirrorTracks] = useState(true)\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Breakpoint split view options\n        {handleClose ? (\n          <IconButton\n            className={classes.closeButton}\n            onClick={() => {\n              handleClose()\n            }}\n          >\n            <CloseIcon />\n          </IconButton>\n        ) : null}\n      </DialogTitle>\n      <Divider />\n\n      <DialogContent>\n        <FormControlLabel\n          className={classes.block}\n          control={\n            <Checkbox\n              checked={copyTracks}\n              onChange={() => setCopyTracks(val => !val)}\n            />\n          }\n          label=\"Copy tracks into the new view\"\n        />\n\n        <FormControlLabel\n          className={classes.block}\n          control={\n            <Checkbox\n              checked={mirrorTracks}\n              onChange={() => setMirrorTracks(val => !val)}\n            />\n          }\n          label=\"Mirror tracks vertically in vertically stacked view\"\n        />\n      </DialogContent>\n      <DialogActions>\n        <Button\n          onClick={() => {\n            const { view } = model\n            const session = getSession(model)\n\n            const viewSnapshot = viewType.snapshotFromBreakendFeature(\n              feature,\n              view,\n            )\n            viewSnapshot.views[0].offsetPx -= view.width / 2 + 100\n            viewSnapshot.views[1].offsetPx -= view.width / 2 + 100\n            viewSnapshot.featureData = feature\n            const viewTracks: any = getSnapshot(view.tracks)\n            viewSnapshot.views[0].tracks = viewTracks\n            viewSnapshot.views[1].tracks = mirrorTracks\n              ? viewTracks.slice().reverse()\n              : viewTracks\n\n            session.addView('BreakpointSplitView', viewSnapshot)\n\n            handleClose()\n          }}\n          variant=\"contained\"\n          color=\"primary\"\n          autoFocus\n        >\n          OK\n        </Button>\n        <Button\n          onClick={() => {\n            handleClose()\n          }}\n          color=\"secondary\"\n          variant=\"contained\"\n          autoFocus\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n}\nexport default observer(BreakendOptionDialog)\n","/* eslint-disable @typescript-eslint/no-explicit-any */\nimport React, { useState } from 'react'\nimport {\n  Divider,\n  Link,\n  Paper,\n  FormControlLabel,\n  Checkbox,\n  TextField,\n  Typography,\n} from '@material-ui/core'\nimport SimpleFeature, {\n  SimpleFeatureSerialized,\n} from '@jbrowse/core/util/simpleFeature'\nimport { DataGrid } from '@mui/x-data-grid'\nimport { observer } from 'mobx-react'\nimport { getSession } from '@jbrowse/core/util'\nimport { getEnv } from 'mobx-state-tree'\nimport {\n  FeatureDetails,\n  BaseCard,\n} from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'\nimport BreakendOptionDialog from './BreakendOptionDialog'\nimport { parseBreakend } from '@gmod/vcf'\n\nfunction VariantSamples(props: any) {\n  const [filter, setFilter] = useState<any>({})\n  const [showFilters, setShowFilters] = useState(false)\n  const { feature } = props\n\n  const { samples = {} } = feature\n  const preFilteredRows: any = Object.entries(samples)\n  if (!preFilteredRows.length) {\n    return null\n  }\n  const infoFields = ['sample', ...Object.keys(preFilteredRows[0][1])].map(\n    field => ({\n      field,\n    }),\n  )\n  let error\n  let rows = []\n  const filters = Object.keys(filter)\n\n  // catch some error thrown from regex\n  // note: maps all values into a string, if this is not done rows are not\n  // sortable by the data-grid\n  try {\n    rows = preFilteredRows\n      .map((row: any) => ({\n        ...Object.fromEntries(\n          Object.entries(row[1]).map(entry => [entry[0], String(entry[1])]),\n        ),\n        sample: row[0],\n        id: row[0],\n      }))\n      .filter((row: any) => {\n        return filters.length\n          ? filters.every(key => {\n              const val = row[key]\n              const currFilter = filter[key]\n              return currFilter ? val.match(new RegExp(currFilter, 'i')) : true\n            })\n          : true\n      })\n  } catch (e) {\n    error = e\n  }\n  // disableSelectionOnClick helps avoid\n  // https://github.com/mui-org/material-ui-x/issues/1197\n  return (\n    <BaseCard {...props} title=\"Samples\">\n      {error ? <Typography color=\"error\">{`${error}`}</Typography> : null}\n\n      <FormControlLabel\n        control={\n          <Checkbox\n            checked={showFilters}\n            onChange={() => setShowFilters(f => !f)}\n          />\n        }\n        label=\"Show sample filters\"\n      />\n      {showFilters ? (\n        <>\n          <Typography>\n            These filters can use a plain text search or regex style query, e.g.\n            in the genotype field, entering 1 will query for all genotypes that\n            include the first alternate allele e.g. 0|1 or 1|1, entering\n            [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33\n          </Typography>\n          {infoFields.map(({ field }) => {\n            return (\n              <TextField\n                key={`filter-${field}`}\n                placeholder={`Filter ${field}`}\n                value={filter[field] || ''}\n                onChange={event =>\n                  setFilter({ ...filter, [field]: event.target.value })\n                }\n              />\n            )\n          })}\n        </>\n      ) : null}\n      <div style={{ height: 600, width: '100%', overflow: 'auto' }}>\n        <DataGrid\n          rows={rows}\n          columns={infoFields}\n          rowHeight={20}\n          headerHeight={25}\n          disableSelectionOnClick\n          disableColumnMenu\n        />\n      </div>\n    </BaseCard>\n  )\n}\n\nfunction BreakendPanel(props: {\n  locStrings: string[]\n  model: any\n  feature: SimpleFeatureSerialized\n}) {\n  const { model, locStrings, feature } = props\n  const session = getSession(model)\n  const { pluginManager } = getEnv(session)\n  const [breakpointDialog, setBreakpointDialog] = useState(false)\n  let viewType\n\n  try {\n    viewType = pluginManager.getViewType('BreakpointSplitView')\n  } catch (e) {\n    // ignore\n  }\n\n  const simpleFeature = new SimpleFeature(feature)\n  return (\n    <BaseCard {...props} title=\"Breakends\">\n      <Typography>Link to linear view of breakend endpoints</Typography>\n      <ul>\n        {locStrings.map(locString => (\n          <li key={`${JSON.stringify(locString)}`}>\n            <Link\n              href=\"#\"\n              onClick={(event: any) => {\n                event.preventDefault()\n                const { view } = model\n                if (view) {\n                  view.navToLocString?.(locString)\n                } else {\n                  session.notify(\n                    'No view associated with this feature detail panel anymore',\n                    'warning',\n                  )\n                }\n              }}\n            >\n              {`LGV - ${locString}`}\n            </Link>\n          </li>\n        ))}\n      </ul>\n      {viewType ? (\n        <div>\n          <Typography>\n            Launch split views with breakend source and target\n          </Typography>\n          <ul>\n            {locStrings.map(locString => (\n              <li key={`${JSON.stringify(locString)}`}>\n                <Link\n                  href=\"#\"\n                  onClick={(event: any) => {\n                    event.preventDefault()\n                    setBreakpointDialog(true)\n                  }}\n                >\n                  {`${feature.refName}:${feature.start} // ${locString} (split view)`}\n                </Link>\n              </li>\n            ))}\n          </ul>\n          {breakpointDialog ? (\n            <BreakendOptionDialog\n              model={model}\n              feature={simpleFeature}\n              viewType={viewType}\n              handleClose={() => {\n                setBreakpointDialog(false)\n              }}\n            />\n          ) : null}\n        </div>\n      ) : null}\n    </BaseCard>\n  )\n}\n\nfunction VariantFeatureDetails(props: any) {\n  const { model } = props\n  const { featureData, descriptions } = model\n  const feat = JSON.parse(JSON.stringify(featureData))\n  const { samples, ...rest } = feat\n  const basicDescriptions = {\n    CHROM: 'chromosome: An identifier from the reference genome',\n    POS: 'position: The reference position, with the 1st base having position 1',\n    ID: 'identifier: Semi-colon separated list of unique identifiers where available',\n    REF: 'reference base(s): Each base must be one of A,C,G,T,N (case insensitive).',\n    ALT: 'alternate base(s): Comma-separated list of alternate non-reference alleles',\n    QUAL: 'quality: Phred-scaled quality score for the assertion made in ALT',\n    FILTER:\n      'filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail',\n  }\n\n  return (\n    <Paper data-testid=\"variant-side-drawer\">\n      <FeatureDetails\n        feature={rest}\n        descriptions={{ ...basicDescriptions, ...descriptions }}\n        {...props}\n      />\n      <Divider />\n      {feat.type === 'breakend' ? (\n        <BreakendPanel\n          feature={feat}\n          locStrings={feat.ALT.map(\n            (alt: string) => parseBreakend(alt).MatePosition,\n          )}\n          model={model}\n        />\n      ) : null}\n      {feat.type === 'translocation' ? (\n        <BreakendPanel\n          feature={feat}\n          model={model}\n          locStrings={[`${feat.INFO.CHR2[0]}:${feat.INFO.END}`]}\n        />\n      ) : null}\n      <VariantSamples feature={feat} {...props} />\n    </Paper>\n  )\n}\n\nexport default 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