@jbrowse/plugin-alignments 1.6.6 → 1.6.7

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

@@ -1 +1 @@
-{"version":3,"file":"plugin-alignments.cjs.development.js","sources":["../../../node_modules/regenerator-runtime/runtime.js","../src/BamAdapter/MismatchParser.ts","../src/CramAdapter/configSchema.ts","../src/CramAdapter/index.ts","../src/BamAdapter/configSchema.ts","../src/BamAdapter/index.ts","../src/HtsgetBamAdapter/configSchema.ts","../src/HtsgetBamAdapter/index.ts","../src/SNPCoverageAdapter/configSchema.ts","../src/util.ts","../src/SNPCoverageAdapter/SNPCoverageAdapter.ts","../src/SNPCoverageAdapter/index.ts","../src/SNPCoverageRenderer/configSchema.js","../src/SNPCoverageRenderer/SNPCoverageRenderer.ts","../src/SNPCoverageRenderer/index.ts","../src/PileupRenderer/sortUtil.ts","../src/PileupRenderer/PileupLayoutSession.ts","../src/PileupRenderer/PileupRenderer.tsx","../src/PileupRenderer/components/PileupRendering.tsx","../src/PileupRenderer/configSchema.ts","../src/PileupRenderer/index.ts","../src/LinearAlignmentsDisplay/models/configSchema.ts","../src/LinearAlignmentsDisplay/models/model.tsx","../src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx","../src/LinearAlignmentsDisplay/index.ts","../src/LinearSNPCoverageDisplay/models/configSchema.ts","../src/LinearSNPCoverageDisplay/components/Tooltip.tsx","../src/shared.ts","../src/LinearSNPCoverageDisplay/models/model.ts","../src/LinearSNPCoverageDisplay/index.ts","../src/LinearPileupDisplay/configSchema.ts","../src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx","../src/LinearPileupDisplay/model.ts","../src/LinearPileupDisplay/index.ts","../src/AlignmentsTrack/index.ts","../src/AlignmentsFeatureDetail/index.ts","../src/PileupRPC/rpcMethods.ts","../src/index.ts","../src/CramAdapter/CramSlightlyLazyFeature.ts","../src/CramAdapter/CramAdapter.ts","../src/BamAdapter/BamSlightlyLazyFeature.ts","../src/BamAdapter/BamAdapter.ts","../src/HtsgetBamAdapter/HtsgetBamAdapter.ts","../src/LinearPileupDisplay/components/ColorByTag.tsx","../src/LinearPileupDisplay/components/FilterByTag.tsx","../src/LinearPileupDisplay/components/SortByTag.tsx","../src/LinearPileupDisplay/components/SetFeatureHeight.tsx","../src/LinearPileupDisplay/components/SetMaxHeight.tsx","../src/LinearPileupDisplay/components/ColorByModifications.tsx","../src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx"],"sourcesContent":["/**\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 { revcom } from '@jbrowse/core/util'\nexport interface Mismatch {\n  qual?: number\n  start: number\n  length: number\n  type: string\n  base: string\n  altbase?: string\n  seq?: string\n  cliplen?: number\n}\n\nexport function parseCigar(cigar: string) {\n  return (cigar || '').split(/([MIDNSHPX=])/)\n}\nexport function cigarToMismatches(\n  ops: string[],\n  seq: string,\n  qual?: Buffer,\n): Mismatch[] {\n  let currOffset = 0\n  let seqOffset = 0\n  const mismatches: Mismatch[] = []\n  for (let i = 0; i < ops.length - 1; i += 2) {\n    const len = +ops[i]\n    const op = ops[i + 1]\n    if (op === 'M' || op === '=' || op === 'E') {\n      seqOffset += len\n    }\n    if (op === 'I') {\n      mismatches.push({\n        start: currOffset,\n        type: 'insertion',\n        base: `${len}`,\n        length: 0,\n      })\n      seqOffset += len\n    } else if (op === 'D') {\n      mismatches.push({\n        start: currOffset,\n        type: 'deletion',\n        base: '*',\n        length: len,\n      })\n    } else if (op === 'N') {\n      mismatches.push({\n        start: currOffset,\n        type: 'skip',\n        base: 'N',\n        length: len,\n      })\n    } else if (op === 'X') {\n      const r = seq.slice(seqOffset, seqOffset + len)\n      const q = qual?.slice(seqOffset, seqOffset + len) || []\n\n      for (let j = 0; j < len; j++) {\n        mismatches.push({\n          start: currOffset + j,\n          type: 'mismatch',\n          base: r[j],\n          qual: q[j],\n          length: 1,\n        })\n      }\n      seqOffset += len\n    } else if (op === 'H') {\n      mismatches.push({\n        start: currOffset,\n        type: 'hardclip',\n        base: `H${len}`,\n        cliplen: len,\n        length: 1,\n      })\n    } else if (op === 'S') {\n      mismatches.push({\n        start: currOffset,\n        type: 'softclip',\n        base: `S${len}`,\n        cliplen: len,\n        length: 1,\n      })\n      seqOffset += len\n    }\n\n    if (op !== 'I' && op !== 'S' && op !== 'H') {\n      currOffset += len\n    }\n  }\n  return mismatches\n}\n\n/**\n * parse a SAM MD tag to find mismatching bases of the template versus the reference\n * @returns array of mismatches and their positions\n */\nexport function mdToMismatches(\n  mdstring: string,\n  cigarOps: string[],\n  cigarMismatches: Mismatch[],\n  seq: string,\n  qual?: Buffer,\n): Mismatch[] {\n  const mismatchRecords: Mismatch[] = []\n  let curr: Mismatch = { start: 0, base: '', length: 0, type: 'mismatch' }\n  const skips = cigarMismatches.filter(cigar => cigar.type === 'skip')\n  let lastCigar = 0\n  let lastTemplateOffset = 0\n  let lastRefOffset = 0\n  let lastSkipPos = 0\n\n  // convert a position on the reference sequence to a position\n  // on the template sequence, taking into account hard and soft\n  // clipping of reads\n\n  function nextRecord(): void {\n    mismatchRecords.push(curr)\n\n    // get a new mismatch record ready\n    curr = {\n      start: curr.start + curr.length,\n      length: 0,\n      base: '',\n      type: 'mismatch',\n    }\n  }\n\n  function getTemplateCoordLocal(refCoord: number): number {\n    let templateOffset = lastTemplateOffset\n    let refOffset = lastRefOffset\n    for (\n      let i = lastCigar;\n      i < cigarOps.length && refOffset <= refCoord;\n      i += 2, lastCigar = i\n    ) {\n      const len = +cigarOps[i]\n      const op = cigarOps[i + 1]\n      if (op === 'S' || op === 'I') {\n        templateOffset += len\n      } else if (op === 'D' || op === 'P' || op === 'N') {\n        refOffset += len\n      } else if (op !== 'H') {\n        templateOffset += len\n        refOffset += len\n      }\n    }\n    lastTemplateOffset = templateOffset\n    lastRefOffset = refOffset\n\n    return templateOffset - (refOffset - refCoord)\n  }\n\n  // now actually parse the MD string\n  const md = mdstring.match(/(\\d+|\\^[a-z]+|[a-z])/gi) || []\n  for (let i = 0; i < md.length; i++) {\n    const token = md[i]\n    const num = +token\n    if (!Number.isNaN(num)) {\n      curr.start += num\n    } else if (token.startsWith('^')) {\n      curr.length = token.length - 1\n      curr.base = '*'\n      curr.type = 'deletion'\n      curr.seq = token.substring(1)\n      nextRecord()\n    } else {\n      // mismatch\n      for (let j = 0; j < token.length; j += 1) {\n        curr.length = 1\n\n        while (lastSkipPos < skips.length) {\n          const mismatch = skips[lastSkipPos]\n          if (curr.start >= mismatch.start) {\n            curr.start += mismatch.length\n            lastSkipPos++\n          } else {\n            break\n          }\n        }\n        const s = cigarOps ? getTemplateCoordLocal(curr.start) : curr.start\n        curr.base = seq ? seq.substr(s, 1) : 'X'\n        const qualScore = qual?.slice(s, s + 1)[0]\n        if (qualScore) {\n          curr.qual = qualScore\n        }\n        curr.altbase = token\n        nextRecord()\n      }\n    }\n  }\n  return mismatchRecords\n}\n\nexport function getTemplateCoord(refCoord: number, cigarOps: string[]): number {\n  let templateOffset = 0\n  let refOffset = 0\n  for (let i = 0; i < cigarOps.length && refOffset <= refCoord; i += 2) {\n    const len = +cigarOps[i]\n    const op = cigarOps[i + 1]\n    if (op === 'S' || op === 'I') {\n      templateOffset += len\n    } else if (op === 'D' || op === 'P') {\n      refOffset += len\n    } else if (op !== 'H') {\n      templateOffset += len\n      refOffset += len\n    }\n  }\n  return templateOffset - (refOffset - refCoord)\n}\n\nexport function getMismatches(\n  cigarString: string,\n  mdString: string,\n  seq: string,\n  qual?: Buffer,\n): Mismatch[] {\n  let mismatches: Mismatch[] = []\n  let cigarOps: string[] = []\n\n  // parse the CIGAR tag if it has one\n  if (cigarString) {\n    cigarOps = parseCigar(cigarString)\n    mismatches = mismatches.concat(cigarToMismatches(cigarOps, seq, qual))\n  }\n\n  // now let's look for CRAM or MD mismatches\n  if (mdString) {\n    mismatches = mismatches.concat(\n      mdToMismatches(mdString, cigarOps, mismatches, seq, qual),\n    )\n  }\n\n  // uniqify the mismatches\n  const seen: { [index: string]: boolean } = {}\n  return mismatches.filter(m => {\n    const key = `${m.type},${m.start},${m.length}`\n    const s = seen[key]\n    seen[key] = true\n    return !s\n  })\n}\n\n// adapted from minimap2 code static void write_MD_core function\nexport function generateMD(target: string, query: string, cigar: string) {\n  let queryOffset = 0\n  let targetOffset = 0\n  let lengthMD = 0\n  if (!target) {\n    console.warn('no ref supplied to generateMD')\n    return ''\n  }\n  const cigarOps = parseCigar(cigar)\n  let str = ''\n  for (let i = 0; i < cigarOps.length; i += 2) {\n    const len = +cigarOps[i]\n    const op = cigarOps[i + 1]\n    if (op === 'M' || op === 'X' || op === '=') {\n      for (let j = 0; j < len; j++) {\n        if (\n          query[queryOffset + j].toLowerCase() !==\n          target[targetOffset + j].toLowerCase()\n        ) {\n          str += `${lengthMD}${target[targetOffset + j].toUpperCase()}`\n          lengthMD = 0\n        } else {\n          lengthMD++\n        }\n      }\n      queryOffset += len\n      targetOffset += len\n    } else if (op === 'I') {\n      queryOffset += len\n    } else if (op === 'D') {\n      let tmp = ''\n      for (let j = 0; j < len; j++) {\n        tmp += target[targetOffset + j].toUpperCase()\n      }\n      str += `${lengthMD}^${tmp}`\n      lengthMD = 0\n      targetOffset += len\n    } else if (op === 'N') {\n      targetOffset += len\n    } else if (op === 'S') {\n      queryOffset += len\n    }\n  }\n  if (lengthMD > 0) {\n    str += lengthMD\n  }\n  return str\n}\n\n// get relative reference sequence positions for positions given relative to\n// the read sequence\nexport function* getNextRefPos(cigarOps: string[], positions: number[]) {\n  let cigarIdx = 0\n  let readPos = 0\n  let refPos = 0\n\n  for (let i = 0; i < positions.length; i++) {\n    const pos = positions[i]\n    for (; cigarIdx < cigarOps.length && readPos < pos; cigarIdx += 2) {\n      const len = +cigarOps[cigarIdx]\n      const op = cigarOps[cigarIdx + 1]\n      if (op === 'S' || op === 'I') {\n        readPos += len\n      } else if (op === 'D' || op === 'N') {\n        refPos += len\n      } else if (op === 'M' || op === 'X' || op === '=') {\n        readPos += len\n        refPos += len\n      }\n    }\n\n    yield positions[i] - readPos + refPos\n  }\n}\n\nexport function getModificationPositions(\n  mm: string,\n  fseq: string,\n  fstrand: number,\n) {\n  const seq = fstrand === -1 ? revcom(fseq) : fseq\n  return mm\n    .split(';')\n    .filter(mod => !!mod)\n    .map(mod => {\n      const [basemod, ...skips] = mod.split(',')\n\n      // regexes based on parse_mm.pl from hts-specs\n      const matches = basemod.match(/([A-Z])([-+])([^,.?]+)([.?])?/)\n      if (!matches) {\n        throw new Error('bad format for MM tag')\n      }\n      const [, base, strand, typestr] = matches\n\n      // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so\n      // split, and they can also be chemical codes (ChEBI) e.g. C+16061\n      const types = typestr.split(/(\\d+|.)/).filter(f => !!f)\n\n      if (strand === '-') {\n        console.warn('unsupported negative strand modifications')\n        // make sure to return a somewhat matching type even in this case\n        return { type: 'unsupported', positions: [] }\n      }\n\n      // this logic also based on parse_mm.pl from hts-specs is that in the\n      // sequence of the read, if we have a modification type e.g. C+m;2 and a\n      // sequence ACGTACGTAC we skip the two instances of C and go to the last\n      // C\n      return types.map(type => {\n        let i = 0\n        return {\n          type,\n          positions: skips\n            .map(score => +score)\n            .map(delta => {\n              do {\n                if (base === 'N' || base === seq[i]) {\n                  delta--\n                }\n                i++\n              } while (delta >= 0 && i < seq.length)\n              const temp = i - 1\n              return fstrand === -1 ? seq.length - 1 - temp : temp\n            })\n            .sort((a, b) => a - b),\n        }\n      })\n    })\n    .flat()\n}\n\nexport function getModificationTypes(mm: string) {\n  const mods = mm.split(';')\n  return mods\n    .filter(mod => !!mod)\n    .map(mod => {\n      const [basemod] = mod.split(',')\n\n      const matches = basemod.match(/([A-Z])([-+])([^,]+)/)\n      if (!matches) {\n        throw new Error('bad format for MM tag')\n      }\n      const [, , , typestr] = matches\n\n      // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so\n      // split, and they can also be chemical codes (ChEBI) e.g. C+16061\n      return typestr.split(/(\\d+|.)/).filter(f => !!f)\n    })\n    .flat()\n}\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default (pluginManager: PluginManager) => {\n  return types.late(() =>\n    ConfigurationSchema(\n      'CramAdapter',\n      {\n        fetchSizeLimit: {\n          type: 'number',\n          defaultValue: 3_000_000,\n        },\n        cramLocation: {\n          type: 'fileLocation',\n          defaultValue: {\n            uri: '/path/to/my.cram',\n            locationType: 'UriLocation',\n          },\n        },\n        craiLocation: {\n          type: 'fileLocation',\n          defaultValue: {\n            uri: '/path/to/my.cram.crai',\n            locationType: 'UriLocation',\n          },\n        },\n        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),\n      },\n      { explicitlyTyped: true },\n    ),\n  )\n}\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\n\n// locals\nimport configSchemaF from './configSchema'\n\nexport default (pluginManager: PluginManager) => {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'CramAdapter',\n        configSchema: pluginManager.load(configSchemaF),\n        getAdapterClass: () => import('./CramAdapter').then(r => r.default),\n      }),\n  )\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default types.late(() =>\n  ConfigurationSchema(\n    'BamAdapter',\n    {\n      bamLocation: {\n        type: 'fileLocation',\n        defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },\n      },\n      index: ConfigurationSchema('BamIndex', {\n        indexType: {\n          model: types.enumeration('IndexType', ['BAI', 'CSI']),\n          type: 'stringEnum',\n          defaultValue: 'BAI',\n        },\n        location: {\n          type: 'fileLocation',\n          defaultValue: {\n            uri: '/path/to/my.bam.bai',\n            locationType: 'UriLocation',\n          },\n        },\n      }),\n      chunkSizeLimit: {\n        type: 'number',\n        defaultValue: 100_000_000,\n      },\n      fetchSizeLimit: {\n        type: 'number',\n        defaultValue: 5_000_000,\n      },\n      sequenceAdapter: {\n        type: 'frozen',\n        defaultValue: null,\n      },\n    },\n    { explicitlyTyped: true },\n  ),\n)\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport configSchema from './configSchema'\n\nexport default (pluginManager: PluginManager) => {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'BamAdapter',\n        configSchema,\n        getAdapterClass: () => import('./BamAdapter').then(r => r.default),\n      }),\n  )\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default types.late(() =>\n  ConfigurationSchema(\n    'HtsgetBamAdapter',\n    {\n      htsgetBase: {\n        type: 'string',\n        defaultValue: '',\n      },\n      htsgetTrackId: {\n        type: 'string',\n        defaultValue: '',\n      },\n      sequenceAdapter: {\n        type: 'frozen',\n        defaultValue: null,\n      },\n    },\n    { explicitlyTyped: true },\n  ),\n)\n","import configSchema from './configSchema'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\n\nexport default (pluginManager: PluginManager) => {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'HtsgetBamAdapter',\n        adapterMetadata: {\n          category: null,\n          hiddenFromGUI: true,\n          displayName: null,\n          description: null,\n        },\n        configSchema,\n        getAdapterClass: () =>\n          import('./HtsgetBamAdapter').then(r => r.default),\n      }),\n  )\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { types } from 'mobx-state-tree'\n\nexport default (pluginManager: PluginManager) =>\n  types.late(() =>\n    ConfigurationSchema(\n      'SNPCoverageAdapter',\n      {\n        subadapter: pluginManager.pluggableConfigSchemaType('adapter'),\n      },\n      { explicitlyTyped: true },\n    ),\n  )\n","import { Feature } from '@jbrowse/core/util/simpleFeature'\n// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and\n// BAM does not\nexport function getTag(feature: Feature, tag: string) {\n  const tags = feature.get('tags')\n  return tags ? tags[tag] : feature.get(tag)\n}\n\n// use fallback alt tag, used in situations where upper case/lower case tags\n// exist e.g. Mm/MM for base modifications\nexport function getTagAlt(feature: Feature, tag: string, alt: string) {\n  return getTag(feature, tag) || getTag(feature, alt)\n}\n\n// orientation definitions from igv.js, see also\n// https://software.broadinstitute.org/software/igv/interpreting_pair_orientations\nexport const orientationTypes = {\n  fr: {\n    F1R2: 'LR',\n    F2R1: 'LR',\n\n    F1F2: 'LL',\n    F2F1: 'LL',\n\n    R1R2: 'RR',\n    R2R1: 'RR',\n\n    R1F2: 'RL',\n    R2F1: 'RL',\n  } as { [key: string]: string },\n\n  rf: {\n    R1F2: 'LR',\n    R2F1: 'LR',\n\n    R1R2: 'LL',\n    R2R1: 'LL',\n\n    F1F2: 'RR',\n    F2F1: 'RR',\n\n    F1R2: 'RL',\n    F2R1: 'RL',\n  } as { [key: string]: string },\n\n  ff: {\n    F2F1: 'LR',\n    R1R2: 'LR',\n\n    F2R1: 'LL',\n    R1F2: 'LL',\n\n    R2F1: 'RR',\n    F1R2: 'RR',\n\n    R2R1: 'RL',\n    F1F2: 'RL',\n  } as { [key: string]: string },\n}\n\nexport function getColorWGBS(strand: number, base: string) {\n  if (strand === 1) {\n    if (base === 'C') {\n      return '#f00'\n    }\n    if (base === 'T') {\n      return '#00f'\n    }\n  } else if (strand === -1) {\n    if (base === 'G') {\n      return '#f00'\n    }\n    if (base === 'A') {\n      return '#00f'\n    }\n  }\n  return '#888'\n}\n","import {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { AugmentedRegion as Region } from '@jbrowse/core/util/types'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { reduce, filter, toArray } from 'rxjs/operators'\nimport { Observable } from 'rxjs'\nimport { getTag, getTagAlt } from '../util'\nimport {\n  parseCigar,\n  getNextRefPos,\n  getModificationPositions,\n  Mismatch,\n} from '../BamAdapter/MismatchParser'\n\ninterface SNPCoverageOptions extends BaseOptions {\n  filters?: SerializableFilterChain\n}\n\nfunction mismatchLen(mismatch: Mismatch) {\n  return !isInterbase(mismatch.type) ? mismatch.length : 1\n}\n\nfunction isInterbase(type: string) {\n  return type === 'softclip' || type === 'hardclip' || type === 'insertion'\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction inc(bin: any, strand: number, type: string, field: string) {\n  if (!bin[type][field]) {\n    bin[type][field] = { total: 0, strands: { '-1': 0, '0': 0, '1': 0 } }\n  }\n  bin[type][field].total++\n  bin[type][field].strands[strand]++\n}\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction dec(bin: any, strand: number, type: string, field: string) {\n  if (!bin[type][field]) {\n    bin[type][field] = { total: 0, strands: { '-1': 0, '0': 0, '1': 0 } }\n  }\n  bin[type][field].total--\n  bin[type][field].strands[strand]--\n}\n\nexport default class SNPCoverageAdapter extends BaseFeatureDataAdapter {\n  protected async configure() {\n    const subadapterConfig = readConfObject(this.config, 'subadapter')\n    const sequenceConf = readConfObject(this.config, [\n      'subadapter',\n      'sequenceAdapter',\n    ])\n    const dataAdapter = await this.getSubAdapter?.(subadapterConfig)\n\n    const sequenceAdapter = sequenceConf\n      ? await this.getSubAdapter?.(sequenceConf)\n      : undefined\n\n    if (!dataAdapter) {\n      throw new Error('Failed to get subadapter')\n    }\n\n    return {\n      subadapter: dataAdapter.dataAdapter as BaseFeatureDataAdapter,\n      sequenceAdapter: sequenceAdapter?.dataAdapter as\n        | BaseFeatureDataAdapter\n        | undefined,\n    }\n  }\n\n  getFeatures(region: Region, opts: SNPCoverageOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const { subadapter } = await this.configure()\n      let stream = subadapter.getFeatures(region, opts)\n\n      if (opts.filters) {\n        const { filters } = opts\n        stream = stream.pipe(filter(f => filters.passes(f, opts)))\n      }\n\n      const { bins, skipmap } = await this.generateCoverageBins(\n        stream,\n        region,\n        opts,\n      )\n\n      bins.forEach((bin, index) => {\n        observer.next(\n          new SimpleFeature({\n            id: `${this.id}-${region.start}-${index}`,\n            data: {\n              score: bin.total,\n              snpinfo: bin,\n              start: region.start + index,\n              end: region.start + index + 1,\n              refName: region.refName,\n            },\n          }),\n        )\n      })\n\n      // make fake features from the coverage\n      Object.entries(skipmap).forEach(([key, skip]) => {\n        observer.next(\n          new SimpleFeature({\n            id: key,\n            data: {\n              type: 'skip',\n              start: skip.start,\n              end: skip.end,\n              strand: skip.strand,\n              score: skip.score,\n              xs: skip.xs,\n            },\n          }),\n        )\n      })\n\n      observer.complete()\n    }, opts.signal)\n  }\n\n  async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {\n    const { subadapter } = await this.configure()\n    return subadapter.estimateRegionsStats(regions, opts)\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    const { subadapter } = await this.configure()\n    return subadapter.getRefNames(opts)\n  }\n\n  freeResources(/* { region } */): void {}\n\n  /**\n   * Generates coverage bins from features which details\n   * the reference, mismatches, strands, and coverage info\n   * @param features - Features of region to be passed in\n   * @param region - Region\n   * @param bpPerPx - base pairs per pixel\n   * @returns Array of nested frequency tables\n   */\n  async generateCoverageBins(\n    features: Observable<Feature>,\n    region: Region,\n    opts: { bpPerPx?: number; colorBy?: { type: string; tag?: string } },\n  ) {\n    const { colorBy } = opts\n    const { sequenceAdapter } = await this.configure()\n    const { originalRefName, refName, start, end } = region\n    const binMax = Math.ceil(region.end - region.start)\n\n    const skipmap = {} as {\n      [key: string]: {\n        score: number\n        feature: unknown\n        start: number\n        end: number\n        strand: number\n        xs: string\n      }\n    }\n\n    // bins contain cov feature if they contribute to coverage, or noncov which\n    // are interbase or other features that don't contribute to coverage.\n    // delskips are elements that don't contribute to coverage, but should be\n    // reported also (and are not interbase)\n    type BinType = { total: number; strands: { [key: string]: number } }\n\n    // request an extra +1 on the end to get CpG crossing region boundary\n    let regionSeq: string | undefined\n\n    if (sequenceAdapter) {\n      const [feat] = await sequenceAdapter\n        .getFeatures({\n          refName: originalRefName || refName,\n          start,\n          end: end + 1,\n          assemblyName: region.assemblyName,\n        })\n        .pipe(toArray())\n        .toPromise()\n      regionSeq = feat?.get('seq')\n    }\n\n    const bins = await features\n      .pipe(\n        reduce(\n          (bins, feature) => {\n            const cigar = feature.get('CIGAR')\n            const fstart = feature.get('start')\n            const fend = feature.get('end')\n            const fstrand = feature.get('strand')\n            const cigarOps = parseCigar(cigar)\n\n            for (let j = fstart; j < fend + 1; j++) {\n              const i = j - region.start\n              if (i >= 0 && i < binMax) {\n                const bin = bins[i] || {\n                  total: 0,\n                  lowqual: {} as BinType,\n                  cov: {} as BinType,\n                  delskips: {} as BinType,\n                  noncov: {} as BinType,\n                  ref: {} as BinType,\n                }\n                if (j !== fend) {\n                  bin.total++\n                  inc(bin, fstrand, 'ref', 'ref')\n                }\n                bins[i] = bin\n              }\n            }\n\n            if (colorBy?.type === 'modifications') {\n              const seq = feature.get('seq')\n              const mm = getTagAlt(feature, 'MM', 'Mm') || ''\n\n              const ml =\n                (getTagAlt(feature, 'ML', 'Ml') as number[] | string) || []\n\n              const probabilities = ml\n                ? (typeof ml === 'string'\n                    ? ml.split(',').map(e => +e)\n                    : ml\n                  ).map(e => e / 255)\n                : (getTagAlt(feature, 'MP', 'Mp') as string)\n                    .split('')\n                    .map(s => s.charCodeAt(0) - 33)\n                    .map(elt => Math.min(1, elt / 50))\n\n              let probIndex = 0\n              getModificationPositions(mm, seq, fstrand).forEach(\n                ({ type, positions }) => {\n                  const mod = `mod_${type}`\n                  for (const pos of getNextRefPos(cigarOps, positions)) {\n                    const epos = pos + fstart - region.start\n                    if (\n                      epos >= 0 &&\n                      epos < bins.length &&\n                      pos + fstart < fend\n                    ) {\n                      const bin = bins[epos] || {\n                        total: 0,\n                        lowqual: {} as BinType,\n                        cov: {} as BinType,\n                        delskips: {} as BinType,\n                        noncov: {} as BinType,\n                        ref: {} as BinType,\n                      }\n\n                      if (probabilities[probIndex] > 0.5) {\n                        inc(bin, fstrand, 'cov', mod)\n                      } else {\n                        inc(bin, fstrand, 'lowqual', mod)\n                      }\n                    }\n                    probIndex++\n                  }\n                },\n              )\n            }\n\n            // methylation based coloring takes into account both reference\n            // sequence CpG detection and reads\n            else if (colorBy?.type === 'methylation') {\n              if (!regionSeq) {\n                throw new Error(\n                  'no region sequence detected, need sequenceAdapter configuration',\n                )\n              }\n              const seq = feature.get('seq')\n              const mm = getTagAlt(feature, 'MM', 'Mm') || ''\n              const methBins = new Array(region.end - region.start).fill(0)\n\n              getModificationPositions(mm, seq, fstrand).forEach(\n                ({ type, positions }) => {\n                  // we are processing methylation\n                  if (type === 'm') {\n                    for (const pos of getNextRefPos(cigarOps, positions)) {\n                      const epos = pos + fstart - region.start\n                      if (epos >= 0 && epos < methBins.length) {\n                        methBins[epos] = 1\n                      }\n                    }\n                  }\n                },\n              )\n\n              for (let j = fstart; j < fend; j++) {\n                const i = j - region.start\n                if (i >= 0 && i < bins.length - 1) {\n                  const l1 = regionSeq[i].toLowerCase()\n                  const l2 = regionSeq[i + 1].toLowerCase()\n                  const bin = bins[i]\n                  const bin1 = bins[i + 1]\n\n                  // color\n                  if (l1 === 'c' && l2 === 'g') {\n                    if (methBins[i] || methBins[i + 1]) {\n                      inc(bin, fstrand, 'cov', 'meth')\n                      inc(bin1, fstrand, 'cov', 'meth')\n                      dec(bin, fstrand, 'ref', 'ref')\n                      dec(bin1, fstrand, 'ref', 'ref')\n                    } else {\n                      inc(bin, fstrand, 'cov', 'unmeth')\n                      inc(bin1, fstrand, 'cov', 'unmeth')\n                      dec(bin, fstrand, 'ref', 'ref')\n                      dec(bin1, fstrand, 'ref', 'ref')\n                    }\n                  }\n                }\n              }\n            }\n\n            // normal SNP based coloring\n            else {\n              const mismatches = feature.get('mismatches') as\n                | Mismatch[]\n                | undefined\n\n              if (mismatches) {\n                for (let i = 0; i < mismatches.length; i++) {\n                  const mismatch = mismatches[i]\n                  const ms = fstart + mismatch.start\n                  for (let j = ms; j < ms + mismatchLen(mismatch); j++) {\n                    const epos = j - region.start\n                    if (epos >= 0 && epos < bins.length) {\n                      const bin = bins[epos]\n                      const { base, type } = mismatch\n                      const interbase = isInterbase(type)\n                      if (!interbase) {\n                        dec(bin, fstrand, 'ref', 'ref')\n                      } else {\n                        inc(bin, fstrand, 'noncov', type)\n                      }\n\n                      if (type === 'deletion' || type === 'skip') {\n                        inc(bin, fstrand, 'delskips', type)\n                        bin.total--\n                      } else if (!interbase) {\n                        inc(bin, fstrand, 'cov', base)\n                      }\n                    }\n                  }\n                }\n\n                mismatches\n                  .filter(mismatch => mismatch.type === 'skip')\n                  .forEach(mismatch => {\n                    const mstart = feature.get('start') + mismatch.start\n                    const start = mstart\n                    const end = mstart + mismatch.length\n                    const strand = feature.get('strand')\n                    const hash = `${start}_${end}_${strand}`\n                    if (!skipmap[hash]) {\n                      skipmap[hash] = {\n                        feature: feature,\n                        start,\n                        end,\n                        strand,\n                        xs: getTag(feature, 'XS') || getTag(feature, 'TS'),\n                        score: 1,\n                      }\n                    } else {\n                      skipmap[hash].score++\n                    }\n                  })\n              }\n            }\n\n            return bins\n          },\n          [] as {\n            total: number\n            lowqual: BinType\n            cov: BinType\n            delskips: BinType\n            noncov: BinType\n            ref: BinType\n          }[],\n        ),\n      )\n      .toPromise()\n\n    return { bins, skipmap }\n  }\n}\n\nconst { capabilities } = SNPCoverageAdapter\nexport { capabilities }\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport configSchemaFactory from './configSchema'\nimport { capabilities } from './SNPCoverageAdapter'\n\nexport default (pluginManager: PluginManager) => {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'SNPCoverageAdapter',\n        adapterMetadata: {\n          category: null,\n          displayName: null,\n          hiddenFromGUI: true,\n          description: null,\n        },\n        getAdapterClass: () =>\n          import('./SNPCoverageAdapter').then(r => r.default),\n        configSchema: configSchemaFactory(pluginManager),\n        adapterCapabilities: capabilities,\n      }),\n  )\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'SNPCoverageRenderer',\n  {\n    clipColor: {\n      type: 'color',\n      description: 'the color of the clipping marker',\n      defaultValue: 'red',\n    },\n    indicatorThreshold: {\n      type: 'number',\n      description:\n        'the proportion of reads containing a insertion/clip indicator',\n      defaultValue: 0.4,\n    },\n    drawArcs: {\n      type: 'boolean',\n      description: 'Draw sashimi-style arcs for intron features',\n      defaultValue: true,\n    },\n    drawInterbaseCounts: {\n      type: 'boolean',\n      description:\n        'draw count \"upsidedown histogram\" of the interbase events that don\\'t contribute to the coverage count so are not drawn in the normal histogram',\n      defaultValue: true,\n    },\n    drawIndicators: {\n      type: 'boolean',\n      description:\n        'draw a triangular indicator where an event has been detected',\n      defaultValue: true,\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import { createJBrowseTheme } from '@jbrowse/core/ui'\nimport { featureSpanPx, bpSpanPx } from '@jbrowse/core/util'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'\nimport {\n  getOrigin,\n  getScale,\n  ScaleOpts,\n  WiggleBaseRenderer,\n  YSCALEBAR_LABEL_OFFSET,\n} from '@jbrowse/plugin-wiggle'\n\nexport interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {\n  bpPerPx: number\n  height: number\n  highResolutionScaling: number\n  scaleOpts: ScaleOpts\n}\n\nexport interface RenderArgsDeserializedWithFeatures\n  extends RenderArgsDeserialized {\n  features: Map<string, Feature>\n  ticks: { values: number[] }\n  displayCrossHatches: boolean\n  modificationTagMap?: Record<string, string>\n}\n\ntype Counts = {\n  [key: string]: { total: number; strands: { [key: string]: number } }\n}\n\ninterface SNPInfo {\n  cov: Counts\n  noncov: Counts\n  total: number\n}\n\nexport default class SNPCoverageRenderer extends WiggleBaseRenderer {\n  // note: the snps are drawn on linear scale even if the data is drawn in log\n  // scape hence the two different scales being used\n  draw(\n    ctx: CanvasRenderingContext2D,\n    props: RenderArgsDeserializedWithFeatures,\n  ) {\n    const {\n      features,\n      regions,\n      bpPerPx,\n      displayCrossHatches,\n      modificationTagMap = {},\n      scaleOpts,\n      height: unadjustedHeight,\n      theme: configTheme,\n      config: cfg,\n      ticks,\n    } = props\n    const theme = createJBrowseTheme(configTheme)\n    const [region] = regions\n    const width = (region.end - region.start) / bpPerPx\n\n    // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the\n    // wiggle display, and makes the height of the actual drawn area add\n    // \"padding\" to the top and bottom of the display\n    const offset = YSCALEBAR_LABEL_OFFSET\n    const height = unadjustedHeight - offset * 2\n\n    const { domain } = scaleOpts\n    if (!domain) {\n      return\n    }\n    const opts = { ...scaleOpts, range: [0, height] }\n    const viewScale = getScale(opts)\n    const snpViewScale = getScale({\n      ...opts,\n      range: [0, height],\n      scaleType: 'linear',\n    })\n    // clipping and insertion indicators, uses a smaller height/2 scale\n    const indicatorViewScale = getScale({\n      ...opts,\n      range: [0, height / 2],\n      scaleType: 'linear',\n    })\n    const originY = getOrigin(scaleOpts.scaleType)\n    const snpOriginY = getOrigin('linear')\n\n    const indicatorThreshold = readConfObject(cfg, 'indicatorThreshold')\n    const drawInterbaseCounts = readConfObject(cfg, 'drawInterbaseCounts')\n    const drawArcs = readConfObject(cfg, 'drawArcs')\n    const drawIndicators = readConfObject(cfg, 'drawIndicators')\n\n    // get the y coordinate that we are plotting at, this can be log scale\n    const toY = (n: number) => height - (viewScale(n) || 0) + offset\n    const toHeight = (n: number) => toY(originY) - toY(n)\n\n    // this is always linear scale, even when plotted on top of log scale\n    const snpToY = (n: number) => height - (snpViewScale(n) || 0) + offset\n    const indicatorToY = (n: number) =>\n      height - (indicatorViewScale(n) || 0) + offset\n    const snpToHeight = (n: number) => snpToY(snpOriginY) - snpToY(n)\n    const indicatorToHeight = (n: number) =>\n      indicatorToY(snpOriginY) - indicatorToY(n)\n\n    const colorForBase: { [key: string]: string } = {\n      A: theme.palette.bases.A.main,\n      C: theme.palette.bases.C.main,\n      G: theme.palette.bases.G.main,\n      T: theme.palette.bases.T.main,\n      total: 'lightgrey',\n      insertion: 'purple',\n      softclip: 'blue',\n      hardclip: 'red',\n      meth: 'red',\n      unmeth: 'blue',\n      ref: 'lightgrey',\n    }\n\n    const feats = [...features.values()]\n    const coverage = feats.filter(f => f.get('type') !== 'skip')\n    const skips = feats.filter(f => f.get('type') === 'skip')\n\n    // Use two pass rendering, which helps in visualizing the SNPs at higher\n    // bpPerPx First pass: draw the gray background\n    ctx.fillStyle = colorForBase.total\n    for (let i = 0; i < coverage.length; i++) {\n      const feature = coverage[i]\n      const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)\n      const w = rightPx - leftPx + 0.3\n      const score = feature.get('score') as number\n      ctx.fillRect(leftPx, toY(score), w, toHeight(score))\n    }\n\n    // Keep track of previous total which we will use it to draw the interbase\n    // indicator (if there is a sudden clip, there will be no read coverage but\n    // there will be \"clip\" coverage) at that position beyond the read. if the\n    // clip is right at a block boundary then prevTotal will not be available,\n    // so this is a best attempt to plot interbase indicator at the \"cliffs\"\n    let prevTotal = 0\n\n    // extraHorizontallyFlippedOffset is used to draw interbase items, which\n    // are located to the left when forward and right when reversed\n    const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0\n\n    // Second pass: draw the SNP data, and add a minimum feature width of 1px\n    // which can be wider than the actual bpPerPx This reduces overdrawing of\n    // the grey background over the SNPs\n\n    for (let i = 0; i < coverage.length; i++) {\n      const feature = coverage[i]\n      const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)\n\n      const snpinfo = feature.get('snpinfo') as SNPInfo\n      const w = Math.max(rightPx - leftPx + 0.3, 1)\n      const totalScore = snpinfo.total\n      const keys = Object.keys(snpinfo.cov).sort()\n\n      let curr = 0\n      for (let i = 0; i < keys.length; i++) {\n        const base = keys[i]\n        const { total } = snpinfo.cov[base]\n        ctx.fillStyle =\n          colorForBase[base] ||\n          modificationTagMap[base.replace('mod_', '')] ||\n          '#888'\n        ctx.fillRect(leftPx, snpToY(total + curr), w, snpToHeight(total))\n        curr += total\n      }\n\n      const interbaseEvents = Object.keys(snpinfo.noncov)\n      const indicatorHeight = 4.5\n      if (drawInterbaseCounts) {\n        let curr = 0\n        for (let i = 0; i < interbaseEvents.length; i++) {\n          const base = interbaseEvents[i]\n          const { total } = snpinfo.noncov[base]\n          ctx.fillStyle = colorForBase[base]\n          ctx.fillRect(\n            leftPx - 0.6 + extraHorizontallyFlippedOffset,\n            indicatorHeight + indicatorToHeight(curr),\n            1.2,\n            indicatorToHeight(total),\n          )\n          curr += total\n        }\n      }\n\n      if (drawIndicators) {\n        let accum = 0\n        let max = 0\n        let maxBase = ''\n        for (let i = 0; i < interbaseEvents.length; i++) {\n          const base = interbaseEvents[i]\n          const { total } = snpinfo.noncov[base]\n          accum += total\n          if (total > max) {\n            max = total\n            maxBase = base\n          }\n        }\n\n        // avoid drawing a bunch of indicators if coverage is very low e.g.\n        // less than 7, uses the prev total in the case of the \"cliff\"\n        const indicatorComparatorScore = Math.max(totalScore, prevTotal)\n        if (\n          accum > indicatorComparatorScore * indicatorThreshold &&\n          indicatorComparatorScore > 7\n        ) {\n          ctx.fillStyle = colorForBase[maxBase]\n          ctx.beginPath()\n          const l = leftPx + extraHorizontallyFlippedOffset\n          ctx.moveTo(l - 3.5, 0)\n          ctx.lineTo(l + 3.5, 0)\n          ctx.lineTo(l, indicatorHeight)\n          ctx.fill()\n        }\n      }\n      prevTotal = totalScore\n    }\n\n    if (drawArcs) {\n      for (let i = 0; i < skips.length; i++) {\n        const f = skips[i]\n        const [left, right] = bpSpanPx(\n          f.get('start'),\n          f.get('end'),\n          region,\n          bpPerPx,\n        )\n\n        ctx.beginPath()\n        const str = f.get('strand') as number\n        const xs = f.get('xs') as string\n        const pos = 'rgba(255,200,200,0.7)'\n        const neg = 'rgba(200,200,255,0.7)'\n        const neutral = 'rgba(200,200,200,0.7)'\n\n        if (xs === '+') {\n          ctx.strokeStyle = pos\n        } else if (xs === '-') {\n          ctx.strokeStyle = neg\n        } else if (str === 1) {\n          ctx.strokeStyle = pos\n        } else if (str === -1) {\n          ctx.strokeStyle = neg\n        } else {\n          ctx.strokeStyle = neutral\n        }\n\n        ctx.lineWidth = Math.log(f.get('score') + 1)\n        ctx.moveTo(left, height - offset * 2)\n        ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2)\n        ctx.stroke()\n      }\n    }\n\n    if (displayCrossHatches) {\n      ctx.lineWidth = 1\n      ctx.strokeStyle = 'rgba(140,140,140,0.8)'\n      ticks.values.forEach(tick => {\n        ctx.beginPath()\n        ctx.moveTo(0, Math.round(toY(tick)))\n        ctx.lineTo(width, Math.round(toY(tick)))\n        ctx.stroke()\n      })\n    }\n  }\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport ConfigSchema from './configSchema'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport SNPCoverageRenderer from './SNPCoverageRenderer'\n\nimport { WiggleRendering } from '@jbrowse/plugin-wiggle'\n\nexport const configSchema = ConfigurationSchema(\n  'SNPCoverageRenderer',\n  {},\n  { baseConfiguration: ConfigSchema, explicitlyTyped: true },\n)\n\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addRendererType(\n    () =>\n      new SNPCoverageRenderer({\n        name: 'SNPCoverageRenderer',\n        ReactComponent: WiggleRendering,\n        configSchema,\n        pluginManager,\n      }),\n  )\n}\n","import { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { doesIntersect2 } from '@jbrowse/core/util/range'\nimport { Mismatch } from '../BamAdapter/MismatchParser'\n\ninterface SortObject {\n  pos: number\n  type: string\n  tag?: string\n}\nexport const sortFeature = (\n  features: Map<string, Feature>,\n  sortedBy: SortObject,\n) => {\n  const featureArray = Array.from(features.values())\n  const featuresInCenterLine: Feature[] = []\n  const featuresOutsideCenter: Feature[] = []\n  const { pos, type } = sortedBy\n\n  // only sort on features that intersect center line, append those outside post-sort\n  featureArray.forEach(innerArray => {\n    const feature = innerArray\n    const start = feature.get('start')\n    const end = feature.get('end')\n    if (doesIntersect2(pos - 1, pos, start, end)) {\n      featuresInCenterLine.push(innerArray)\n    } else {\n      featuresOutsideCenter.push(innerArray)\n    }\n  })\n\n  const isCram = featureArray.length ? featureArray[0].get('tags') : false\n  switch (type) {\n    case 'Start location': {\n      featuresInCenterLine.sort((a, b) => a.get('start') - b.get('start'))\n      break\n    }\n\n    case 'tag': {\n      const tag = sortedBy.tag as string\n      const getTag = (f: Feature, t: string) => {\n        return isCram ? f.get('tags')[t] : f.get(t)\n      }\n      const isString =\n        featuresInCenterLine[0] &&\n        typeof getTag(featuresInCenterLine[0], tag) === 'string'\n      if (isString) {\n        featuresInCenterLine.sort((a, b) =>\n          getTag(b, tag).localeCompare(getTag(a, tag)),\n        )\n      } else {\n        featuresInCenterLine.sort(\n          (a, b) => (getTag(b, tag) || 0) - (getTag(a, tag) || 0),\n        )\n      }\n      break\n    }\n\n    // first sort all mismatches, then all reference bases at the end\n    case 'Base pair': {\n      const baseSortArray: [string, Mismatch][] = []\n      featuresInCenterLine.forEach(feature => {\n        const mismatches: Mismatch[] = feature.get('mismatches')\n        mismatches.forEach(mismatch => {\n          const start = feature.get('start')\n          const offset = start + mismatch.start + 1\n          const consuming =\n            mismatch.type === 'insertion' || mismatch.type === 'softclip'\n          const len = consuming ? 0 : mismatch.length\n          if (pos >= offset && pos < offset + len) {\n            baseSortArray.push([feature.id(), mismatch])\n          }\n        })\n      })\n\n      const baseMap = new Map(baseSortArray)\n      featuresInCenterLine.sort((a, b) => {\n        const aMismatch = baseMap.get(a.id())\n        const bMismatch = baseMap.get(b.id())\n        const acode = bMismatch && bMismatch.base.toUpperCase()\n        const bcode = aMismatch && aMismatch.base.toUpperCase()\n        if (acode === bcode && acode === '*') {\n          // @ts-ignore\n          return aMismatch.length - bMismatch.length\n        }\n        return (\n          (acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0)\n        )\n      })\n\n      break\n    }\n\n    // sorts positive strands then negative strands\n    case 'Read strand': {\n      featuresInCenterLine.sort((a, b) =>\n        a.get('strand') <= b.get('strand') ? 1 : -1,\n      )\n      break\n    }\n  }\n\n  const sortedMap = new Map(\n    featuresInCenterLine\n      .concat(featuresOutsideCenter)\n      .map(feature => [feature.id(), feature]),\n  )\n\n  return sortedMap\n}\n","import deepEqual from 'fast-deep-equal'\nimport { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'\nimport SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'\nimport GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout'\nimport MultiLayout from '@jbrowse/core/util/layouts/MultiLayout'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nexport interface PileupLayoutSessionProps {\n  config: AnyConfigurationModel\n  bpPerPx: number\n  filters: SerializableFilterChain\n  sortedBy: unknown\n  showSoftClip: unknown\n}\n\ntype MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>\ninterface CachedPileupLayout {\n  layout: MyMultiLayout\n  config: AnyConfigurationModel\n  filters: SerializableFilterChain\n  sortedBy: unknown\n  showSoftClip: boolean\n}\n// Sorting and revealing soft clip changes the layout of Pileup renderer\n// Adds extra conditions to see if cached layout is valid\nexport class PileupLayoutSession extends LayoutSession {\n  sortedBy: unknown\n\n  showSoftClip = false\n\n  constructor(args: PileupLayoutSessionProps) {\n    super(args)\n    this.config = args.config\n  }\n\n  cachedLayoutIsValid(cachedLayout: CachedPileupLayout) {\n    return (\n      super.cachedLayoutIsValid(cachedLayout) &&\n      this.showSoftClip === cachedLayout.showSoftClip &&\n      deepEqual(this.sortedBy, cachedLayout.sortedBy)\n    )\n  }\n\n  cachedLayout: CachedPileupLayout | undefined\n\n  get layout(): MyMultiLayout {\n    if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {\n      this.cachedLayout = {\n        layout: this.makeLayout(),\n        config: readConfObject(this.config),\n        filters: this.filters,\n        sortedBy: this.sortedBy,\n        showSoftClip: this.showSoftClip,\n      }\n    }\n    return this.cachedLayout.layout\n  }\n}\n","import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'\nimport { toArray } from 'rxjs/operators'\nimport BoxRendererType, {\n  RenderArgs,\n  RenderArgsSerialized,\n  RenderArgsDeserialized as BoxRenderArgsDeserialized,\n  RenderResults,\n  ResultsSerialized,\n  ResultsDeserialized,\n} from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'\nimport { Theme } from '@material-ui/core'\nimport { createJBrowseTheme } from '@jbrowse/core/ui'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { bpSpanPx, iterMap } from '@jbrowse/core/util'\nimport Color from 'color'\nimport { Region } from '@jbrowse/core/util/types'\nimport { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils'\nimport { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout'\nimport { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\n// locals\nimport {\n  Mismatch,\n  parseCigar,\n  getModificationPositions,\n  getNextRefPos,\n} from '../BamAdapter/MismatchParser'\nimport { sortFeature } from './sortUtil'\nimport { getTagAlt, orientationTypes } from '../util'\nimport {\n  PileupLayoutSession,\n  PileupLayoutSessionProps,\n} from './PileupLayoutSession'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\n\nfunction getColorBaseMap(theme: Theme) {\n  return {\n    A: theme.palette.bases.A.main,\n    C: theme.palette.bases.C.main,\n    G: theme.palette.bases.G.main,\n    T: theme.palette.bases.T.main,\n    deletion: '#808080', // gray\n  }\n}\n\nexport interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {\n  colorBy?: { type: string; tag?: string }\n  colorTagMap?: Record<string, string>\n  modificationTagMap?: Record<string, string>\n  sortedBy?: {\n    type: string\n    pos: number\n    refName: string\n    assemblyName: string\n    tag?: string\n  }\n  showSoftClip: boolean\n  highResolutionScaling: number\n}\n\nexport interface RenderArgsDeserializedWithFeaturesAndLayout\n  extends RenderArgsDeserialized {\n  features: Map<string, Feature>\n  layout: BaseLayout<Feature>\n  regionSequence?: string\n}\n\ninterface LayoutRecord {\n  feature: Feature\n  leftPx: number\n  rightPx: number\n  topPx: number\n  heightPx: number\n}\n\nconst alignmentColoring: { [key: string]: string } = {\n  color_fwd_strand_not_proper: '#ECC8C8',\n  color_rev_strand_not_proper: '#BEBED8',\n  color_fwd_strand: '#EC8B8B',\n  color_rev_strand: '#8F8FD8',\n  color_fwd_missing_mate: '#D11919',\n  color_rev_missing_mate: '#1919D1',\n  color_fwd_diff_chr: '#000',\n  color_rev_diff_chr: '#969696',\n  color_pair_lr: '#c8c8c8',\n  color_pair_rr: 'navy',\n  color_pair_rl: 'teal',\n  color_pair_ll: 'green',\n  color_nostrand: '#c8c8c8',\n  color_interchrom: 'orange',\n  color_longinsert: 'red',\n  color_shortinsert: 'pink',\n}\n\ninterface LayoutFeature {\n  heightPx: number\n  topPx: number\n  feature: Feature\n}\n\nfunction shouldDrawMismatches(type?: string) {\n  return !['methylation', 'modifications'].includes(type || '')\n}\n\nexport default class PileupRenderer extends BoxRendererType {\n  supportsSVG = true\n\n  // get width and height of chars the height is an approximation: width\n  // letter M is approximately the height\n  getCharWidthHeight(ctx: CanvasRenderingContext2D) {\n    const charWidth = ctx.measureText('A').width\n    const charHeight = ctx.measureText('M').width\n    return { charWidth, charHeight }\n  }\n\n  layoutFeature({\n    feature,\n    layout,\n    bpPerPx,\n    region,\n    showSoftClip,\n    heightPx,\n    displayMode,\n  }: {\n    feature: Feature\n    layout: BaseLayout<Feature>\n    bpPerPx: number\n    region: Region\n    showSoftClip?: boolean\n    heightPx: number\n    displayMode: string\n  }): LayoutRecord | null {\n    let expansionBefore = 0\n    let expansionAfter = 0\n\n    // Expand the start and end of feature when softclipping enabled\n    if (showSoftClip) {\n      const mismatches = feature.get('mismatches') as Mismatch[]\n      const seq = feature.get('seq') as string\n      if (seq) {\n        for (let i = 0; i < mismatches.length; i += 1) {\n          const { type, start, cliplen = 0 } = mismatches[i]\n          if (type === 'softclip') {\n            start === 0\n              ? (expansionBefore = cliplen)\n              : (expansionAfter = cliplen)\n          }\n        }\n      }\n    }\n\n    const [leftPx, rightPx] = bpSpanPx(\n      feature.get('start') - expansionBefore,\n      feature.get('end') + expansionAfter,\n      region,\n      bpPerPx,\n    )\n\n    if (displayMode === 'compact') {\n      heightPx /= 3\n    }\n    if (feature.get('refName') !== region.refName) {\n      throw new Error(\n        `feature ${feature.id()} is not on the current region's reference sequence ${\n          region.refName\n        }`,\n      )\n    }\n    const topPx = layout.addRect(\n      feature.id(),\n      feature.get('start') - expansionBefore,\n      feature.get('end') + expansionAfter,\n      heightPx,\n    )\n    if (topPx === null) {\n      return null\n    }\n\n    return {\n      feature,\n      leftPx,\n      rightPx,\n      topPx: displayMode === 'collapse' ? 0 : topPx,\n      heightPx,\n    }\n  }\n\n  // expands region for clipping to use. possible improvement: use average read\n  // size to set the heuristic maxClippingSize expansion (e.g. short reads\n  // don't have to expand a softclipping size a lot, but long reads might)\n  getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized) {\n    const { config, showSoftClip } = renderArgs\n\n    const maxClippingSize = readConfObject(config, 'maxClippingSize')\n    const { start, end } = region\n    const len = end - start\n    const bpExpansion = Math.max(\n      len,\n      showSoftClip ? Math.round(maxClippingSize) : 0,\n    )\n\n    return {\n      ...region,\n      start: Math.floor(Math.max(start - bpExpansion, 0)),\n      end: Math.ceil(end + bpExpansion),\n    }\n  }\n\n  colorByOrientation(feature: Feature, config: AnyConfigurationModel) {\n    return alignmentColoring[\n      this.getOrientation(feature, config) || 'color_nostrand'\n    ]\n  }\n\n  getOrientation(feature: Feature, config: AnyConfigurationModel) {\n    const orientationType = readConfObject(config, 'orientationType') as\n      | 'fr'\n      | 'ff'\n      | 'rf'\n    const type = orientationTypes[orientationType]\n    const orientation = type[feature.get('pair_orientation') as string]\n    const map: { [key: string]: string } = {\n      LR: 'color_pair_lr',\n      RR: 'color_pair_rr',\n      RL: 'color_pair_rl',\n      LL: 'color_pair_ll',\n    }\n    return map[orientation]\n  }\n\n  colorByInsertSize(feature: Feature, _config: AnyConfigurationModel) {\n    return feature.get('is_paired') &&\n      feature.get('seq_id') !== feature.get('next_seq_id')\n      ? '#555'\n      : `hsl(${Math.abs(feature.get('template_length')) / 10},50%,50%)`\n  }\n\n  colorByStranded(feature: Feature, _config: AnyConfigurationModel) {\n    const flags = feature.get('flags')\n    const strand = feature.get('strand')\n    // is paired\n    if (flags & 1) {\n      const revflag = flags & 64\n      const flipper = revflag ? -1 : 1\n      // proper pairing\n      if (flags & 2) {\n        return strand * flipper === 1 ? 'color_rev_strand' : 'color_fwd_strand'\n      }\n      if (feature.get('multi_segment_next_segment_unmapped')) {\n        return strand * flipper === 1\n          ? 'color_rev_missing_mate'\n          : 'color_fwd_missing_mate'\n      }\n      if (feature.get('seq_id') === feature.get('next_seq_id')) {\n        return strand * flipper === 1\n          ? 'color_rev_strand_not_proper'\n          : 'color_fwd_strand_not_proper'\n      }\n      // should only leave aberrant chr\n      return strand === 1 ? 'color_fwd_diff_chr' : 'color_rev_diff_chr'\n    }\n    return strand === 1 ? 'color_fwd_strand' : 'color_rev_strand'\n  }\n\n  colorByPerBaseQuality(\n    ctx: CanvasRenderingContext2D,\n    feat: LayoutFeature,\n    _config: AnyConfigurationModel,\n    region: Region,\n    bpPerPx: number,\n  ) {\n    const { feature, topPx, heightPx } = feat\n    const qual: string = feature.get('qual') || ''\n    const scores = qual.split(' ').map(val => +val)\n    const cigarOps = parseCigar(feature.get('CIGAR'))\n    const width = 1 / bpPerPx\n    const start = feature.get('start')\n\n    for (let i = 0, j = 0, k = 0; k < scores.length; i += 2, k++) {\n      const len = +cigarOps[i]\n      const op = cigarOps[i + 1]\n      if (op === 'S' || op === 'I') {\n        k += len\n      } else if (op === 'D' || op === 'N') {\n        j += len\n      } else if (op === 'M' || op === 'X' || op === '=') {\n        for (let m = 0; m < len; m++) {\n          const score = scores[k + m]\n          ctx.fillStyle = `hsl(${score === 255 ? 150 : score * 1.5},55%,50%)`\n          const [leftPx] = bpSpanPx(\n            start + j + m,\n            start + j + m + 1,\n            region,\n            bpPerPx,\n          )\n          ctx.fillRect(leftPx, topPx, width + 0.5, heightPx)\n        }\n        j += len\n      }\n    }\n  }\n\n  // ML stores probabilities as array of numerics and MP is scaled phred scores\n  // https://github.com/samtools/hts-specs/pull/418/files#diff-e765c6479316309f56b636f88189cdde8c40b854c7bdcce9ee7fe87a4e76febcR596\n  //\n  // if we have ML or Ml, it is an 8bit probability, divide by 255\n  //\n  // if we have MP or Mp it is phred scaled ASCII, which can go up to 90 but\n  // has very high likelihood basecalls at that point, we really only care\n  // about low qual calls <20 approx\n  //\n  colorByModifications(\n    ctx: CanvasRenderingContext2D,\n    layoutFeature: LayoutFeature,\n    _config: AnyConfigurationModel,\n    region: Region,\n    bpPerPx: number,\n    props: RenderArgsDeserializedWithFeaturesAndLayout,\n  ) {\n    const { feature, topPx, heightPx } = layoutFeature\n    const { modificationTagMap = {} } = props\n\n    const mm = (getTagAlt(feature, 'MM', 'Mm') as string) || ''\n\n    const ml = (getTagAlt(feature, 'ML', 'Ml') as number[] | string) || []\n\n    const probabilities = ml\n      ? (typeof ml === 'string' ? ml.split(',').map(e => +e) : ml).map(\n          e => e / 255,\n        )\n      : (getTagAlt(feature, 'MP', 'Mp') as string)\n          .split('')\n          .map(s => s.charCodeAt(0) - 33)\n          .map(elt => Math.min(1, elt / 50))\n\n    const cigar = feature.get('CIGAR')\n    const start = feature.get('start')\n    const end = feature.get('end')\n    const seq = feature.get('seq')\n    const strand = feature.get('strand')\n    const cigarOps = parseCigar(cigar)\n\n    const modifications = getModificationPositions(mm, seq, strand)\n\n    // probIndex applies across multiple modifications e.g.\n    let probIndex = 0\n    for (let i = 0; i < modifications.length; i++) {\n      const { type, positions } = modifications[i]\n      const col = modificationTagMap[type] || 'black'\n      const base = Color(col)\n      for (const readPos of getNextRefPos(cigarOps, positions)) {\n        if (readPos >= 0 && start + readPos < end) {\n          const [leftPx, rightPx] = bpSpanPx(\n            start + readPos,\n            start + readPos + 1,\n            region,\n            bpPerPx,\n          )\n\n          // give it a little boost of 0.1 to not make them fully\n          // invisible to avoid confusion\n          ctx.fillStyle = base\n            .alpha(probabilities[probIndex] + 0.1)\n            .hsl()\n            .string()\n          ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx)\n        }\n        probIndex++\n      }\n    }\n  }\n\n  // Color by methylation is slightly modified version of color by\n  // modifications\n  //\n  colorByMethylation(\n    ctx: CanvasRenderingContext2D,\n    layoutFeature: LayoutFeature,\n    _config: AnyConfigurationModel,\n    region: Region,\n    bpPerPx: number,\n    props: RenderArgsDeserializedWithFeaturesAndLayout,\n  ) {\n    const { regionSequence } = props\n    const { feature, topPx, heightPx } = layoutFeature\n\n    const mm: string = getTagAlt(feature, 'MM', 'Mm') || ''\n\n    if (!regionSequence) {\n      throw new Error('region sequence required for methylation')\n    }\n\n    const cigar = feature.get('CIGAR')\n    const fstart = feature.get('start')\n    const fend = feature.get('end')\n    const seq = feature.get('seq')\n    const strand = feature.get('strand')\n    const cigarOps = parseCigar(cigar)\n    const { start: rstart, end: rend } = region\n\n    const methBins = new Array(rend - rstart).fill(0)\n    const modifications = getModificationPositions(mm, seq, strand)\n    for (let i = 0; i < modifications.length; i++) {\n      const { type, positions } = modifications[i]\n      if (type === 'm' && positions) {\n        for (const pos of getNextRefPos(cigarOps, positions)) {\n          const epos = pos + fstart - rstart\n          if (epos >= 0 && epos < methBins.length) {\n            methBins[epos] = 1\n          }\n        }\n      }\n    }\n\n    for (let j = fstart; j < fend; j++) {\n      const i = j - rstart\n      if (i >= 0 && i < methBins.length) {\n        const l1 = regionSequence[i].toLowerCase()\n        const l2 = regionSequence[i + 1].toLowerCase()\n\n        // if we are zoomed out, display just a block over the cpg\n        if (bpPerPx > 2) {\n          if (l1 === 'c' && l2 === 'g') {\n            const s = rstart + i\n            const [leftPx, rightPx] = bpSpanPx(s, s + 2, region, bpPerPx)\n            if (methBins[i] || methBins[i + 1]) {\n              ctx.fillStyle = 'red'\n            } else {\n              ctx.fillStyle = 'blue'\n            }\n            ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx)\n          }\n        }\n        // if we are zoomed in, color the c inside the cpg\n        else {\n          // color\n          if (l1 === 'c' && l2 === 'g') {\n            const s = rstart + i\n            const [leftPx, rightPx] = bpSpanPx(s, s + 1, region, bpPerPx)\n            if (methBins[i]) {\n              ctx.fillStyle = 'red'\n            } else {\n              ctx.fillStyle = 'blue'\n            }\n            ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx)\n\n            const [leftPx2, rightPx2] = bpSpanPx(s + 1, s + 2, region, bpPerPx)\n            if (methBins[i + 1]) {\n              ctx.fillStyle = 'red'\n            } else {\n              ctx.fillStyle = 'blue'\n            }\n            ctx.fillRect(leftPx2, topPx, rightPx2 - leftPx2 + 0.5, heightPx)\n          }\n        }\n      }\n    }\n  }\n\n  drawRect(\n    ctx: CanvasRenderingContext2D,\n    feat: LayoutFeature,\n    props: RenderArgsDeserialized,\n  ) {\n    const { regions, bpPerPx } = props\n    const { heightPx, topPx, feature } = feat\n    const [region] = regions\n    const [leftPx, rightPx] = bpSpanPx(\n      feature.get('start'),\n      feature.get('end'),\n      region,\n      bpPerPx,\n    )\n    const flip = region.reversed ? -1 : 1\n    const strand = feature.get('strand') * flip\n    if (bpPerPx < 10) {\n      if (strand === -1) {\n        ctx.beginPath()\n        ctx.moveTo(leftPx - 5, topPx + heightPx / 2)\n        ctx.lineTo(leftPx, topPx + heightPx)\n        ctx.lineTo(rightPx, topPx + heightPx)\n        ctx.lineTo(rightPx, topPx)\n        ctx.lineTo(leftPx, topPx)\n        ctx.closePath()\n        ctx.fill()\n      } else {\n        ctx.beginPath()\n        ctx.moveTo(leftPx, topPx)\n        ctx.lineTo(leftPx, topPx + heightPx)\n        ctx.lineTo(rightPx, topPx + heightPx)\n        ctx.lineTo(rightPx + 5, topPx + heightPx / 2)\n        ctx.lineTo(rightPx, topPx)\n        ctx.closePath()\n        ctx.fill()\n      }\n    } else {\n      ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx)\n    }\n  }\n\n  drawAlignmentRect(\n    ctx: CanvasRenderingContext2D,\n    feat: LayoutFeature,\n    props: RenderArgsDeserializedWithFeaturesAndLayout & {\n      defaultColor: boolean\n    },\n  ) {\n    const {\n      defaultColor,\n      config,\n      bpPerPx,\n      regions,\n      colorBy,\n      colorTagMap = {},\n    } = props\n    const { tag = '', type: colorType = '' } = colorBy || {}\n    const { feature } = feat\n    const region = regions[0]\n\n    // first pass for simple color changes that change the color of the\n    // alignment\n    switch (colorType) {\n      case 'insertSize':\n        ctx.fillStyle = this.colorByInsertSize(feature, config)\n        break\n      case 'strand':\n        ctx.fillStyle = feature.get('strand') === -1 ? '#8F8FD8' : '#EC8B8B'\n        break\n      case 'mappingQuality':\n        ctx.fillStyle = `hsl(${feature.get('mq')},50%,50%)`\n        break\n\n      case 'pairOrientation':\n        ctx.fillStyle = this.colorByOrientation(feature, config)\n        break\n      case 'stranded':\n        ctx.fillStyle = alignmentColoring[this.colorByStranded(feature, config)]\n        break\n      case 'xs':\n      case 'tag': {\n        const tags = feature.get('tags')\n        const val = tags ? tags[tag] : feature.get(tag)\n\n        // special for for XS/TS tag\n        if (tag === 'XS' || tag === 'TS') {\n          const map: { [key: string]: string | undefined } = {\n            '-': 'color_rev_strand',\n            '+': 'color_fwd_strand',\n          }\n          ctx.fillStyle = alignmentColoring[map[val] || 'color_nostrand']\n        }\n\n        // lower case 'ts' from minimap2 is flipped from xs\n        if (tag === 'ts') {\n          const map: { [key: string]: string } = {\n            '-':\n              feature.get('strand') === -1\n                ? 'color_fwd_strand'\n                : 'color_rev_strand',\n            '+':\n              feature.get('strand') === -1\n                ? 'color_rev_strand'\n                : 'color_fwd_strand',\n          }\n          ctx.fillStyle = alignmentColoring[map[val] || 'color_nostrand']\n        }\n\n        // tag is not one of the autofilled tags, has color-value pairs from\n        // fetchValues\n        else {\n          const foundValue = colorTagMap[val]\n          ctx.fillStyle = foundValue || alignmentColoring['color_nostrand']\n        }\n        break\n      }\n      case 'insertSizeAndPairOrientation':\n        break\n\n      case 'normal':\n      default:\n        if (defaultColor) {\n          // avoid a readConfObject call here\n          ctx.fillStyle = '#c8c8c8'\n        } else {\n          ctx.fillStyle = readConfObject(config, 'color', { feature })\n        }\n        break\n    }\n\n    this.drawRect(ctx, feat, props)\n\n    // second pass for color types that render per-base things that go over the\n    // existing drawing\n    switch (colorType) {\n      case 'perBaseQuality':\n        this.colorByPerBaseQuality(ctx, feat, config, region, bpPerPx)\n        break\n\n      case 'modifications':\n        this.colorByModifications(ctx, feat, config, region, bpPerPx, props)\n        break\n\n      case 'methylation':\n        this.colorByMethylation(ctx, feat, config, region, bpPerPx, props)\n        break\n    }\n  }\n\n  drawMismatches(\n    ctx: CanvasRenderingContext2D,\n    feat: LayoutFeature,\n    props: RenderArgsDeserializedWithFeaturesAndLayout,\n    theme: Theme,\n    colorForBase: { [key: string]: string },\n    opts: {\n      mismatchAlpha?: boolean\n      drawSNPs?: boolean\n      drawIndels?: boolean\n      minSubfeatureWidth: number\n      largeInsertionIndicatorScale: number\n      charWidth: number\n      charHeight: number\n    },\n  ) {\n    const {\n      minSubfeatureWidth: minWidth,\n      largeInsertionIndicatorScale,\n      mismatchAlpha,\n      drawSNPs = true,\n      drawIndels = true,\n      charWidth,\n      charHeight,\n    } = opts\n    const { bpPerPx, regions } = props\n    const { heightPx, topPx, feature } = feat\n    const [region] = regions\n    const start = feature.get('start')\n\n    const pxPerBp = Math.min(1 / bpPerPx, 2)\n    const w = Math.max(minWidth, pxPerBp)\n    const mismatches: Mismatch[] = feature.get('mismatches')\n    const heightLim = charHeight - 2\n\n    function getAlphaColor(baseColor: string, mismatch: { qual?: number }) {\n      let color = baseColor\n      if (mismatchAlpha && mismatch.qual !== undefined) {\n        color = Color(baseColor)\n          .alpha(Math.min(1, mismatch.qual / 50))\n          .hsl()\n          .string()\n      }\n      return color\n    }\n\n    // extraHorizontallyFlippedOffset is used to draw interbase items, which\n    // are located to the left when forward and right when reversed\n    const extraHorizontallyFlippedOffset = region.reversed\n      ? 1 / bpPerPx + 1\n      : -1\n\n    // two pass rendering: first pass, draw all the mismatches except wide\n    // insertion markers\n    for (let i = 0; i < mismatches.length; i += 1) {\n      const mismatch = mismatches[i]\n      const mstart = start + mismatch.start\n      const mlen = mismatch.length\n      const mbase = mismatch.base\n      const [leftPx, rightPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx)\n      const widthPx = Math.max(minWidth, Math.abs(leftPx - rightPx))\n      if (mismatch.type === 'mismatch' && drawSNPs) {\n        const baseColor = colorForBase[mismatch.base] || '#888'\n\n        ctx.fillStyle = getAlphaColor(baseColor, mismatch)\n\n        ctx.fillRect(leftPx, topPx, widthPx, heightPx)\n\n        if (widthPx >= charWidth && heightPx >= heightLim) {\n          // normal SNP coloring\n          ctx.fillStyle = getAlphaColor(\n            theme.palette.getContrastText(baseColor),\n            mismatch,\n          )\n          ctx.fillText(\n            mbase,\n            leftPx + (widthPx - charWidth) / 2 + 1,\n            topPx + heightPx,\n          )\n        }\n      } else if (mismatch.type === 'deletion' && drawIndels) {\n        const baseColor = colorForBase.deletion\n        ctx.fillStyle = baseColor\n        ctx.fillRect(leftPx, topPx, widthPx, heightPx)\n        const txt = `${mismatch.length}`\n        const rect = ctx.measureText(txt)\n        if (widthPx >= rect.width && heightPx >= heightLim) {\n          ctx.fillStyle = theme.palette.getContrastText(baseColor)\n          ctx.fillText(\n            txt,\n            leftPx + (rightPx - leftPx) / 2 - rect.width / 2,\n            topPx + heightPx,\n          )\n        }\n      } else if (mismatch.type === 'insertion' && drawIndels) {\n        ctx.fillStyle = 'purple'\n        const pos = leftPx + extraHorizontallyFlippedOffset\n        const len = +mismatch.base || mismatch.length\n        const insW = Math.max(minWidth, Math.min(1.2, 1 / bpPerPx))\n        if (len < 10) {\n          ctx.fillRect(pos, topPx, insW, heightPx)\n          if (1 / bpPerPx >= charWidth) {\n            ctx.fillRect(pos - insW, topPx, insW * 3, 1)\n            ctx.fillRect(pos - insW, topPx + heightPx - 1, insW * 3, 1)\n          }\n          if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {\n            ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx)\n          }\n        }\n      } else if (mismatch.type === 'hardclip' || mismatch.type === 'softclip') {\n        ctx.fillStyle = mismatch.type === 'hardclip' ? 'red' : 'blue'\n        const pos = leftPx + extraHorizontallyFlippedOffset\n        ctx.fillRect(pos, topPx, w, heightPx)\n        if (1 / bpPerPx >= charWidth) {\n          ctx.fillRect(pos - w, topPx, w * 3, 1)\n          ctx.fillRect(pos - w, topPx + heightPx - 1, w * 3, 1)\n        }\n        if (widthPx >= charWidth && heightPx >= heightLim) {\n          ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx)\n        }\n      } else if (mismatch.type === 'skip') {\n        // fix to avoid bad rendering note that this was also related to chrome\n        // bug https://bugs.chromium.org/p/chromium/issues/detail?id=1131528\n        // also affected firefox ref #1236 #2750\n        if (leftPx + widthPx > 0) {\n          // make small exons more visible when zoomed far out\n          const adjustPx = widthPx - (bpPerPx > 10 ? 1.5 : 0)\n          ctx.clearRect(leftPx, topPx, adjustPx, heightPx)\n          ctx.fillStyle = '#333'\n          ctx.fillRect(\n            Math.max(0, leftPx),\n            topPx + heightPx / 2 - 1,\n            adjustPx + (leftPx < 0 ? leftPx : 0),\n            2,\n          )\n        }\n      }\n    }\n\n    // second pass, draw wide insertion markers on top\n    if (drawIndels) {\n      for (let i = 0; i < mismatches.length; i += 1) {\n        const mismatch = mismatches[i]\n        const mstart = start + mismatch.start\n        const mlen = mismatch.length\n        const [leftPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx)\n        const len = +mismatch.base || mismatch.length\n        const txt = `${len}`\n        if (mismatch.type === 'insertion' && len >= 10) {\n          if (bpPerPx > largeInsertionIndicatorScale) {\n            ctx.fillStyle = 'purple'\n            ctx.fillRect(leftPx - 1, topPx, 2, heightPx)\n          } else if (heightPx > charHeight) {\n            const rect = ctx.measureText(txt)\n            const padding = 5\n            ctx.fillStyle = 'purple'\n            ctx.fillRect(\n              leftPx - rect.width / 2 - padding,\n              topPx,\n              rect.width + 2 * padding,\n              heightPx,\n            )\n            ctx.fillStyle = 'white'\n            ctx.fillText(txt, leftPx - rect.width / 2, topPx + heightPx)\n          } else {\n            const padding = 2\n            ctx.fillStyle = 'purple'\n            ctx.fillRect(leftPx - padding, topPx, 2 * padding, heightPx)\n          }\n        }\n      }\n    }\n  }\n\n  drawSoftClipping(\n    ctx: CanvasRenderingContext2D,\n    feat: LayoutFeature,\n    props: RenderArgsDeserializedWithFeaturesAndLayout,\n    config: AnyConfigurationModel,\n    theme: Theme,\n  ) {\n    const { feature, topPx, heightPx } = feat\n    const { regions, bpPerPx } = props\n    const [region] = regions\n    const minFeatWidth = readConfObject(config, 'minSubfeatureWidth')\n    const mismatches: Mismatch[] = feature.get('mismatches')\n    const seq = feature.get('seq')\n    const { charWidth, charHeight } = this.getCharWidthHeight(ctx)\n    const colorForBase: { [key: string]: string } = {\n      A: theme.palette.bases.A.main,\n      C: theme.palette.bases.C.main,\n      G: theme.palette.bases.G.main,\n      T: theme.palette.bases.T.main,\n      deletion: '#808080', // gray\n    }\n\n    // Display all bases softclipped off in lightened colors\n    if (seq) {\n      mismatches\n        .filter(mismatch => mismatch.type === 'softclip')\n        .forEach(mismatch => {\n          const softClipLength = mismatch.cliplen || 0\n          const s = feature.get('start')\n          const softClipStart =\n            mismatch.start === 0 ? s - softClipLength : s + mismatch.start\n\n          for (let k = 0; k < softClipLength; k += 1) {\n            const base = seq.charAt(k + mismatch.start)\n\n            // If softclip length+start is longer than sequence, no need to\n            // continue showing base\n            if (!base) {\n              return\n            }\n\n            const [softClipLeftPx, softClipRightPx] = bpSpanPx(\n              softClipStart + k,\n              softClipStart + k + 1,\n              region,\n              bpPerPx,\n            )\n            const softClipWidthPx = Math.max(\n              minFeatWidth,\n              Math.abs(softClipLeftPx - softClipRightPx),\n            )\n\n            // Black accounts for IUPAC ambiguity code bases such as N that\n            // show in soft clipping\n            const baseColor = colorForBase[base] || '#000000'\n            ctx.fillStyle = baseColor\n            ctx.fillRect(softClipLeftPx, topPx, softClipWidthPx, heightPx)\n\n            if (softClipWidthPx >= charWidth && heightPx >= charHeight - 5) {\n              ctx.fillStyle = theme.palette.getContrastText(baseColor)\n              ctx.fillText(\n                base,\n                softClipLeftPx + (softClipWidthPx - charWidth) / 2 + 1,\n                topPx + heightPx,\n              )\n            }\n          }\n        })\n    }\n  }\n\n  async makeImageData(\n    ctx: CanvasRenderingContext2D,\n    layoutRecords: (LayoutFeature | null)[],\n    props: RenderArgsDeserializedWithFeaturesAndLayout,\n  ) {\n    const { layout, config, showSoftClip, colorBy, theme: configTheme } = props\n    const mismatchAlpha = readConfObject(config, 'mismatchAlpha')\n    const minSubfeatureWidth = readConfObject(config, 'minSubfeatureWidth')\n    const insertScale = readConfObject(config, 'largeInsertionIndicatorScale')\n    const defaultColor = readConfObject(config, 'color') === '#f0f'\n\n    const theme = createJBrowseTheme(configTheme)\n    const colorForBase = getColorBaseMap(theme)\n    if (!layout) {\n      throw new Error(`layout required`)\n    }\n    if (!layout.addRect) {\n      throw new Error('invalid layout object')\n    }\n    ctx.font = 'bold 10px Courier New,monospace'\n\n    const { charWidth, charHeight } = this.getCharWidthHeight(ctx)\n    layoutRecords.forEach(feat => {\n      if (feat === null) {\n        return\n      }\n\n      this.drawAlignmentRect(ctx, feat, {\n        ...props,\n        defaultColor,\n      })\n      this.drawMismatches(ctx, feat, props, theme, colorForBase, {\n        mismatchAlpha,\n        drawSNPs: shouldDrawMismatches(colorBy?.type),\n        drawIndels: shouldDrawMismatches(colorBy?.type),\n        largeInsertionIndicatorScale: insertScale,\n        minSubfeatureWidth,\n        charWidth,\n        charHeight,\n      })\n      if (showSoftClip) {\n        this.drawSoftClipping(ctx, feat, props, config, theme)\n      }\n    })\n  }\n\n  // we perform a full layout before render as a separate method because the\n  // layout determines the height of the canvas that we use to render\n  layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout) {\n    const {\n      layout,\n      features,\n      sortedBy,\n      config,\n      bpPerPx,\n      showSoftClip,\n      regions,\n    } = props\n    const [region] = regions\n    if (!layout) {\n      throw new Error(`layout required`)\n    }\n    if (!layout.addRect) {\n      throw new Error('invalid layout object')\n    }\n\n    const featureMap =\n      sortedBy?.type && region.start === sortedBy.pos\n        ? sortFeature(features, sortedBy)\n        : features\n\n    const heightPx = readConfObject(config, 'height')\n    const displayMode = readConfObject(config, 'displayMode')\n    const layoutRecords = iterMap(\n      featureMap.values(),\n      feature =>\n        this.layoutFeature({\n          feature,\n          layout,\n          bpPerPx,\n          region,\n          showSoftClip,\n          heightPx,\n          displayMode,\n        }),\n      featureMap.size,\n    )\n    return layoutRecords\n  }\n\n  async render(renderProps: RenderArgsDeserialized) {\n    const { sessionId, bpPerPx, regions, adapterConfig } = renderProps\n    const { sequenceAdapter } = adapterConfig\n    const features = await this.getFeatures(renderProps)\n    const layout = this.createLayoutInWorker(renderProps)\n\n    const layoutRecords = this.layoutFeats({ ...renderProps, features, layout })\n    const [region] = regions\n    let regionSequence: string | undefined\n    const { end, start, originalRefName, refName } = region\n\n    if (sequenceAdapter) {\n      const { dataAdapter } = await getAdapter(\n        this.pluginManager,\n        sessionId,\n        sequenceAdapter,\n      )\n\n      const feats = await (dataAdapter as BaseFeatureDataAdapter)\n        .getFeatures({\n          ...region,\n          refName: originalRefName || refName,\n          end: region.end + 1,\n        })\n        .pipe(toArray())\n        .toPromise()\n      regionSequence = feats[0]?.get('seq')\n    }\n\n    const width = (end - start) / bpPerPx\n    const height = Math.max(layout.getTotalHeight(), 1)\n\n    const res = await renderToAbstractCanvas(\n      width,\n      height,\n      renderProps,\n      (ctx: CanvasRenderingContext2D) =>\n        this.makeImageData(ctx, layoutRecords, {\n          ...renderProps,\n          layout,\n          features,\n          regionSequence,\n        }),\n    )\n\n    const results = await super.render({\n      ...renderProps,\n      ...res,\n      features,\n      layout,\n      height,\n      width,\n    })\n\n    return {\n      ...results,\n      ...res,\n      features,\n      layout,\n      height,\n      width,\n      maxHeightReached: layout.maxHeightReached,\n    }\n  }\n\n  createSession(args: PileupLayoutSessionProps) {\n    return new PileupLayoutSession(args)\n  }\n}\n\nexport type {\n  RenderArgs,\n  RenderArgsSerialized,\n  RenderResults,\n  ResultsSerialized,\n  ResultsDeserialized,\n}\n","import { Region } from '@jbrowse/core/util/types'\nimport { PrerenderedCanvas } from '@jbrowse/core/ui'\nimport { bpSpanPx } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\nimport React, { MouseEvent, useRef, useState, useEffect } from 'react'\nimport type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view'\n\n// used so that user can click-away-from-feature below the laid out features\n// (issue #1248)\nconst canvasPadding = 100\nfunction PileupRendering(props: {\n  blockKey: string\n  displayModel: BaseLinearDisplayModel\n  width: number\n  height: number\n  regions: Region[]\n  bpPerPx: number\n  sortedBy?: { type: string; pos: number; refName: string }\n  colorBy?: { type: string; tag?: string }\n  onMouseMove?: (event: React.MouseEvent, featureId: string | undefined) => void\n}) {\n  const {\n    onMouseMove,\n    blockKey,\n    displayModel,\n    width,\n    height,\n    regions,\n    bpPerPx,\n    sortedBy,\n    colorBy,\n  } = props\n  const { selectedFeatureId, featureIdUnderMouse, contextMenuFeature } =\n    displayModel\n\n  const [region] = regions\n  const highlightOverlayCanvas = useRef<HTMLCanvasElement>(null)\n  const [mouseIsDown, setMouseIsDown] = useState(false)\n  const [movedDuringLastMouseDown, setMovedDuringLastMouseDown] =\n    useState(false)\n  useEffect(() => {\n    const canvas = highlightOverlayCanvas.current\n    if (!canvas) {\n      return\n    }\n    const ctx = canvas.getContext('2d')\n    if (!ctx) {\n      return\n    }\n    ctx.clearRect(0, 0, canvas.width, canvas.height)\n    const selectedRect = selectedFeatureId\n      ? displayModel.getFeatureByID?.(blockKey, selectedFeatureId)\n      : undefined\n    if (selectedRect) {\n      const [leftBp, topPx, rightBp, bottomPx] = selectedRect\n      const [leftPx, rightPx] = bpSpanPx(leftBp, rightBp, region, bpPerPx)\n      const rectTop = Math.round(topPx)\n      const rectHeight = Math.round(bottomPx - topPx)\n      ctx.shadowColor = '#222266'\n      ctx.shadowBlur = 10\n      ctx.lineJoin = 'bevel'\n      ctx.lineWidth = 2\n      ctx.strokeStyle = '#00b8ff'\n      ctx.strokeRect(\n        leftPx - 2,\n        rectTop - 2,\n        rightPx - leftPx + 4,\n        rectHeight + 4,\n      )\n      ctx.clearRect(leftPx, rectTop, rightPx - leftPx, rectHeight)\n    }\n    const highlightedFeature = featureIdUnderMouse || contextMenuFeature?.id()\n    const highlightedRect = highlightedFeature\n      ? displayModel.getFeatureByID?.(blockKey, highlightedFeature)\n      : undefined\n    if (highlightedRect) {\n      const [leftBp, topPx, rightBp, bottomPx] = highlightedRect\n      const [leftPx, rightPx] = bpSpanPx(leftBp, rightBp, region, bpPerPx)\n      const rectTop = Math.round(topPx)\n      const rectHeight = Math.round(bottomPx - topPx)\n      ctx.fillStyle = '#0003'\n      ctx.fillRect(leftPx, rectTop, rightPx - leftPx, rectHeight)\n    }\n  }, [\n    bpPerPx,\n    region,\n    blockKey,\n    selectedFeatureId,\n    displayModel,\n    featureIdUnderMouse,\n    contextMenuFeature,\n  ])\n\n  function onMouseDown(event: MouseEvent) {\n    setMouseIsDown(true)\n    setMovedDuringLastMouseDown(false)\n    callMouseHandler('MouseDown', event)\n  }\n\n  function onMouseEnter(event: MouseEvent) {\n    callMouseHandler('MouseEnter', event)\n  }\n\n  function onMouseOut(event: MouseEvent) {\n    callMouseHandler('MouseOut', event)\n    callMouseHandler('MouseLeave', event)\n  }\n\n  function onMouseOver(event: MouseEvent) {\n    callMouseHandler('MouseOver', event)\n  }\n\n  function onMouseUp(event: MouseEvent) {\n    setMouseIsDown(false)\n    callMouseHandler('MouseUp', event)\n  }\n\n  function onClick(event: MouseEvent) {\n    if (!movedDuringLastMouseDown) {\n      callMouseHandler('Click', event)\n    }\n  }\n\n  function onMouseLeave(event: MouseEvent) {\n    callMouseHandler('MouseOut', event)\n    callMouseHandler('MouseLeave', event)\n  }\n\n  function onContextMenu(event: MouseEvent) {\n    callMouseHandler('ContextMenu', event)\n  }\n\n  function mouseMove(event: MouseEvent) {\n    if (mouseIsDown) {\n      setMovedDuringLastMouseDown(true)\n    }\n    let offsetX = 0\n    let offsetY = 0\n    const canvas = highlightOverlayCanvas.current\n    if (canvas) {\n      const { left, top } = canvas.getBoundingClientRect()\n      offsetX = left\n      offsetY = top\n    }\n    offsetX = event.clientX - offsetX\n    offsetY = event.clientY - offsetY\n    const px = region.reversed ? width - offsetX : offsetX\n    const clientBp = region.start + bpPerPx * px\n\n    const featIdUnderMouse = displayModel.getFeatureOverlapping(\n      blockKey,\n      clientBp,\n      offsetY,\n    )\n\n    if (onMouseMove) {\n      onMouseMove(event, featIdUnderMouse)\n    }\n  }\n\n  function callMouseHandler(handlerName: string, event: MouseEvent) {\n    // @ts-ignore\n    // eslint-disable-next-line react/destructuring-assignment\n    const featureHandler = props[`onFeature${handlerName}`]\n    // @ts-ignore\n    // eslint-disable-next-line react/destructuring-assignment\n    const canvasHandler = props[`on${handlerName}`]\n    if (featureHandler && featureIdUnderMouse) {\n      featureHandler(event, featureIdUnderMouse)\n    } else if (canvasHandler) {\n      canvasHandler(event, featureIdUnderMouse)\n    }\n  }\n\n  const canvasWidth = Math.ceil(width)\n  // need to call this in render so we get the right observer behavior\n  return (\n    <div\n      className=\"PileupRendering\"\n      data-testid={`pileup-${\n        sortedBy || colorBy\n          ? `${sortedBy?.type || ''}${colorBy?.type || ''}${colorBy?.tag || ''}`\n          : 'normal'\n      }`}\n      style={{ position: 'relative', width: canvasWidth, height }}\n    >\n      <PrerenderedCanvas\n        {...props}\n        style={{ position: 'absolute', left: 0, top: 0 }}\n      />\n      <canvas\n        data-testid=\"pileup_overlay_canvas\"\n        width={canvasWidth}\n        height={height + canvasPadding}\n        style={{ position: 'absolute', left: 0, top: 0 }}\n        className=\"highlightOverlayCanvas\"\n        ref={highlightOverlayCanvas}\n        onMouseDown={event => onMouseDown(event)}\n        onMouseEnter={event => onMouseEnter(event)}\n        onMouseOut={event => onMouseOut(event)}\n        onMouseOver={event => onMouseOver(event)}\n        onMouseUp={event => onMouseUp(event)}\n        onMouseLeave={event => onMouseLeave(event)}\n        onMouseMove={event => mouseMove(event)}\n        onClick={event => onClick(event)}\n        onContextMenu={event => onContextMenu(event)}\n        onFocus={() => {}}\n        onBlur={() => {}}\n      />\n    </div>\n  )\n}\n\nexport default observer(PileupRendering)\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default ConfigurationSchema(\n  'PileupRenderer',\n  {\n    // default magenta here is used to detect the user has not customized this\n    color: {\n      type: 'color',\n      description: 'the color of each feature in a pileup alignment',\n      defaultValue: '#f0f',\n      contextVariable: ['feature'],\n    },\n    orientationType: {\n      type: 'stringEnum',\n      model: types.enumeration('orientationType', ['fr', 'rf', 'ff']),\n      defaultValue: 'fr',\n      description:\n        'read sequencer orienation. fr is normal \"reads pointing at each other ---> <--- while some other sequencers can use other options',\n    },\n    displayMode: {\n      type: 'stringEnum',\n      model: types.enumeration('displayMode', [\n        'normal',\n        'compact',\n        'collapse',\n      ]),\n      description: 'Alternative display modes',\n      defaultValue: 'normal',\n    },\n    minSubfeatureWidth: {\n      type: 'number',\n      description:\n        'the minimum width in px for a pileup mismatch feature. use for increasing mismatch marker widths when zoomed out to e.g. 1px or 0.5px',\n      defaultValue: 0,\n    },\n    maxHeight: {\n      type: 'integer',\n      description: 'the maximum height to be used in a pileup rendering',\n      defaultValue: 1200,\n    },\n    maxClippingSize: {\n      type: 'integer',\n      description: 'the max clip size to be used in a pileup rendering',\n      defaultValue: 10000,\n    },\n    height: {\n      type: 'number',\n      description: 'the height of each feature in a pileup alignment',\n      defaultValue: 7,\n      contextVariable: ['feature'],\n    },\n    noSpacing: {\n      type: 'boolean',\n      description: 'remove spacing between features',\n      defaultValue: false,\n    },\n    largeInsertionIndicatorScale: {\n      type: 'number',\n      description:\n        'scale at which to draw the large insertion indicators (bp/pixel)',\n      defaultValue: 10,\n    },\n    mismatchAlpha: {\n      type: 'boolean',\n      defaultValue: false,\n      description: 'Fade low quality mismatches',\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport PileupRenderer from './PileupRenderer'\nimport ReactComponent from './components/PileupRendering'\nimport configSchema from './configSchema'\n\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addRendererType(\n    () =>\n      new PileupRenderer({\n        name: 'PileupRenderer',\n        ReactComponent,\n        configSchema,\n        pluginManager,\n      }),\n  )\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nconst configModelFactory = (pluginManager: PluginManager) => {\n  const PileupDisplayConfigSchema = pluginManager.getDisplayType(\n    'LinearPileupDisplay',\n  ).configSchema\n  const SNPCoverageDisplayConfigSchema = pluginManager.getDisplayType(\n    'LinearSNPCoverageDisplay',\n  ).configSchema\n\n  return ConfigurationSchema(\n    'LinearAlignmentsDisplay',\n    {\n      pileupDisplay: PileupDisplayConfigSchema,\n      snpCoverageDisplay: SNPCoverageDisplayConfigSchema,\n    },\n    { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n  )\n}\n\nexport type AlignmentsConfigModel = ReturnType<typeof configModelFactory>\nexport default configModelFactory\n","import React from 'react'\nimport {\n  ConfigurationReference,\n  AnyConfigurationModel,\n  getConf,\n} from '@jbrowse/core/configuration'\nimport { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { MenuItem } from '@jbrowse/core/ui'\nimport { autorun, when } from 'mobx'\nimport { addDisposer, getSnapshot, Instance, types } from 'mobx-state-tree'\nimport { getContainingTrack } from '@jbrowse/core/util'\nimport deepEqual from 'fast-deep-equal'\nimport { AlignmentsConfigModel } from './configSchema'\n\nconst minDisplayHeight = 20\nconst stateModelFactory = (\n  pluginManager: PluginManager,\n  configSchema: AlignmentsConfigModel,\n) => {\n  return types\n    .compose(\n      'LinearAlignmentsDisplay',\n      BaseDisplay,\n      types.model({\n        PileupDisplay: types.maybe(\n          pluginManager.getDisplayType('LinearPileupDisplay').stateModel,\n        ),\n        SNPCoverageDisplay: types.maybe(\n          pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel,\n        ),\n        snpCovHeight: 45,\n        type: types.literal('LinearAlignmentsDisplay'),\n        configuration: ConfigurationReference(configSchema),\n        height: 250,\n        showCoverage: true,\n        showPileup: true,\n        userFeatureScreenDensity: types.maybe(types.number),\n      }),\n    )\n    .volatile(() => ({\n      scrollTop: 0,\n    }))\n    .actions(self => ({\n      toggleCoverage() {\n        self.showCoverage = !self.showCoverage\n      },\n      togglePileup() {\n        self.showPileup = !self.showPileup\n      },\n      setScrollTop(scrollTop: number) {\n        self.scrollTop = scrollTop\n      },\n      setSNPCoverageHeight(n: number) {\n        self.snpCovHeight = n\n      },\n    }))\n    .views(self => {\n      const { trackMenuItems: superTrackMenuItems } = self\n      return {\n        get pileupDisplayConfig() {\n          const conf = getConf(self, 'pileupDisplay')\n          const track = getContainingTrack(self)\n          return {\n            ...conf,\n            type: 'LinearPileupDisplay',\n            name: `${getConf(track, 'name')} pileup`,\n            displayId: `${self.configuration.displayId}_pileup_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this\n          }\n        },\n\n        getFeatureByID(blockKey: string, id: string) {\n          return self.PileupDisplay.getFeatureByID(blockKey, id)\n        },\n        searchFeatureByID(id: string) {\n          return self.PileupDisplay.searchFeatureByID(id)\n        },\n\n        get features() {\n          return self.PileupDisplay.features\n        },\n\n        get DisplayBlurb() {\n          return self.PileupDisplay?.DisplayBlurb\n        },\n\n        get sortedBy() {\n          return self.PileupDisplay.sortedBy\n        },\n        get sortedByPosition() {\n          return self.PileupDisplay.sortedByPosition\n        },\n        get sortedByRefName() {\n          return self.PileupDisplay.sortedByRefName\n        },\n\n        get snpCoverageDisplayConfig() {\n          const conf = getConf(self, 'snpCoverageDisplay')\n          const track = getContainingTrack(self)\n          return {\n            ...conf,\n            type: 'LinearSNPCoverageDisplay',\n            name: `${getConf(track, 'name')} snp coverage`,\n            displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this\n          }\n        },\n\n        trackMenuItems(): MenuItem[] {\n          return [\n            ...superTrackMenuItems(),\n            {\n              type: 'subMenu',\n              label: 'Pileup settings',\n              subMenu: self.PileupDisplay.trackMenuItems(),\n            },\n            {\n              type: 'subMenu',\n              label: 'SNPCoverage settings',\n              subMenu: self.SNPCoverageDisplay.trackMenuItems(),\n            },\n          ]\n        },\n      }\n    })\n    .actions(self => ({\n      setSNPCoverageDisplay(displayConfig: AnyConfigurationModel) {\n        self.SNPCoverageDisplay = {\n          type: 'LinearSNPCoverageDisplay',\n          configuration: displayConfig,\n          height: self.snpCovHeight,\n        }\n      },\n      setUserFeatureScreenDensity(limit: number) {\n        self.PileupDisplay.setUserFeatureScreenDensity(limit)\n        self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit)\n      },\n      setPileupDisplay(displayConfig: AnyConfigurationModel) {\n        self.PileupDisplay = {\n          type: 'LinearPileupDisplay',\n          configuration: displayConfig,\n        }\n      },\n      setHeight(displayHeight: number) {\n        if (displayHeight > minDisplayHeight) {\n          self.height = displayHeight\n        } else {\n          self.height = minDisplayHeight\n        }\n        return self.height\n      },\n      resizeHeight(distance: number) {\n        const oldHeight = self.height\n        const newHeight = this.setHeight(self.height + distance)\n        return newHeight - oldHeight\n      },\n    }))\n    .actions(self => ({\n      afterAttach() {\n        addDisposer(\n          self,\n          autorun(() => {\n            if (!self.SNPCoverageDisplay) {\n              self.setSNPCoverageDisplay(self.snpCoverageDisplayConfig)\n            } else if (\n              !deepEqual(\n                self.snpCoverageDisplayConfig,\n                getSnapshot(self.SNPCoverageDisplay.configuration),\n              )\n            ) {\n              self.SNPCoverageDisplay.setHeight(self.snpCovHeight)\n              self.SNPCoverageDisplay.setConfig(self.snpCoverageDisplayConfig)\n            }\n\n            if (!self.PileupDisplay) {\n              self.setPileupDisplay(self.pileupDisplayConfig)\n            } else if (\n              !deepEqual(\n                self.pileupDisplayConfig,\n                getSnapshot(self.PileupDisplay.configuration),\n              )\n            ) {\n              self.PileupDisplay.setConfig(self.pileupDisplayConfig)\n            }\n\n            // propagate the filterBy setting from pileupdisplay to snpcoverage\n            // note: the snpcoverage display is not able to control filterBy\n            // itself\n            if (\n              self.PileupDisplay.filterBy &&\n              !deepEqual(\n                getSnapshot(self.PileupDisplay.filterBy),\n                getSnapshot(self.SNPCoverageDisplay.filterBy),\n              )\n            ) {\n              self.SNPCoverageDisplay.setFilterBy(\n                getSnapshot(self.PileupDisplay.filterBy),\n              )\n            }\n            if (\n              self.PileupDisplay.colorBy &&\n              !deepEqual(\n                getSnapshot(self.PileupDisplay.colorBy),\n                self.SNPCoverageDisplay.colorBy\n                  ? getSnapshot(self.SNPCoverageDisplay.colorBy)\n                  : {},\n              )\n            ) {\n              self.SNPCoverageDisplay.setColorBy(\n                getSnapshot(self.PileupDisplay.colorBy),\n              )\n            }\n          }),\n        )\n        addDisposer(\n          self,\n          autorun(() => {\n            self.setSNPCoverageHeight(self.SNPCoverageDisplay.height)\n          }),\n        )\n      },\n      async renderSvg(opts: { rasterizeLayers?: boolean }) {\n        const pileupHeight = self.height - self.SNPCoverageDisplay.height\n        await when(() => self.PileupDisplay.ready)\n        return (\n          <>\n            <g>{await self.SNPCoverageDisplay.renderSvg(opts)}</g>\n            <g transform={`translate(0 ${self.SNPCoverageDisplay.height})`}>\n              {\n                await self.PileupDisplay.renderSvg({\n                  ...opts,\n                  overrideHeight: pileupHeight,\n                })\n              }\n            </g>\n          </>\n        )\n      },\n    }))\n}\n\nexport default stateModelFactory\nexport type AlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>\nexport type AlignmentsDisplayModel = Instance<AlignmentsDisplayStateModel>\n","import React from 'react'\nimport { observer } from 'mobx-react'\nimport { getConf } from '@jbrowse/core/configuration'\nimport { ResizeHandle } from '@jbrowse/core/ui'\nimport { makeStyles } from '@material-ui/core'\nimport { AlignmentsDisplayModel } from '../models/model'\n\nconst useStyles = makeStyles(() => ({\n  resizeHandle: {\n    height: 2,\n    position: 'absolute',\n    zIndex: 2,\n  },\n}))\n\nfunction AlignmentsDisplay({ model }: { model: AlignmentsDisplayModel }) {\n  const { PileupDisplay, SNPCoverageDisplay, showPileup, showCoverage } = model\n  const classes = useStyles()\n  const top = SNPCoverageDisplay.height\n  return (\n    <div\n      data-testid={`display-${getConf(model, 'displayId')}`}\n      style={{ position: 'relative' }}\n    >\n      {showCoverage ? (\n        <>\n          <div data-testid=\"Blockset-snpcoverage\">\n            <SNPCoverageDisplay.RenderingComponent model={SNPCoverageDisplay} />\n          </div>\n          <ResizeHandle\n            onDrag={delta => {\n              SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta)\n              return delta\n            }}\n            className={classes.resizeHandle}\n            style={{\n              top,\n            }}\n          />\n        </>\n      ) : null}\n\n      {showPileup ? (\n        <div\n          data-testid=\"Blockset-pileup\"\n          style={{\n            position: 'absolute',\n            top: showCoverage ? SNPCoverageDisplay.height : 0,\n          }}\n        >\n          <PileupDisplay.RenderingComponent model={PileupDisplay} />\n        </div>\n      ) : null}\n    </div>\n  )\n}\n\nexport default observer(AlignmentsDisplay)\n","import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\nimport PluginManager from '@jbrowse/core/PluginManager'\n// locals\nimport configSchemaFactory from './models/configSchema'\nimport modelFactory from './models/model'\nimport ReactComponent from './components/AlignmentsDisplay'\n\nexport default function (pluginManager: PluginManager) {\n  pluginManager.addDisplayType(() => {\n    const configSchema = configSchemaFactory(pluginManager)\n    return new DisplayType({\n      name: 'LinearAlignmentsDisplay',\n      configSchema,\n      stateModel: modelFactory(pluginManager, configSchema),\n      trackType: 'AlignmentsTrack',\n      viewType: 'LinearGenomeView',\n      ReactComponent,\n    })\n  })\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'\nimport { types } from 'mobx-state-tree'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function SNPCoverageConfigFactory(pluginManager: PluginManager) {\n  const SNPCoverageRendererConfigSchema = pluginManager.getRendererType(\n    'SNPCoverageRenderer',\n  ).configSchema\n\n  return ConfigurationSchema(\n    'LinearSNPCoverageDisplay',\n    {\n      autoscale: {\n        type: 'stringEnum',\n        defaultValue: 'local',\n        model: types.enumeration('Autoscale type', ['local']),\n        description:\n          'performs local autoscaling (no other options for SNP Coverage available)',\n      },\n      minScore: {\n        type: 'number',\n        defaultValue: Number.MIN_VALUE,\n        description: 'minimum value for the y-scale',\n      },\n      maxScore: {\n        type: 'number',\n        description: 'maximum value for the y-scale',\n        defaultValue: Number.MAX_VALUE,\n      },\n      scaleType: {\n        type: 'stringEnum',\n        model: types.enumeration('Scale type', ['linear', 'log']), // todo zscale\n        description: 'The type of scale to use',\n        defaultValue: 'linear',\n      },\n      inverted: {\n        type: 'boolean',\n        description: 'draw upside down',\n        defaultValue: false,\n      },\n\n      multiTicks: {\n        type: 'boolean',\n        description: 'Display multiple values for the ticks',\n        defaultValue: false,\n      },\n\n      renderers: ConfigurationSchema('RenderersConfiguration', {\n        SNPCoverageRenderer: SNPCoverageRendererConfigSchema,\n      }),\n    },\n    { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n  )\n}\n","/* eslint-disable @typescript-eslint/no-explicit-any */\nimport React from 'react'\nimport { observer } from 'mobx-react'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { Tooltip } from '@jbrowse/plugin-wiggle'\n\ntype Count = {\n  [key: string]: {\n    total: number\n    strands: { [key: string]: number }\n  }\n}\n\ntype SNPInfo = {\n  ref: Count\n  cov: Count\n  lowqual: Count\n  noncov: Count\n  delskips: Count\n  total: number\n}\n\nconst en = (n: number) => n.toLocaleString('en-US')\n\nconst TooltipContents = React.forwardRef(\n  ({ feature }: { feature: Feature }, ref: any) => {\n    const start = feature.get('start')\n    const end = feature.get('end')\n    const name = feature.get('refName')\n    const info = feature.get('snpinfo') as SNPInfo\n    const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]\n      .filter(f => !!f)\n      .join(':')\n\n    const total = info?.total\n\n    return (\n      <div ref={ref}>\n        <table>\n          <caption>{loc}</caption>\n          <thead>\n            <tr>\n              <th>Base</th>\n              <th>Count</th>\n              <th>% of Total</th>\n              <th>Strands</th>\n              <th>Source</th>\n            </tr>\n          </thead>\n          <tbody>\n            <tr>\n              <td>Total</td>\n              <td>{total}</td>\n              <td />\n            </tr>\n\n            {Object.entries(info).map(([key, entry]) => {\n              return Object.entries(entry).map(([base, score]) => {\n                const { strands } = score\n                return (\n                  <tr key={base}>\n                    <td>{base.toUpperCase()}</td>\n                    <td>{score.total}</td>\n                    <td>\n                      {base === 'total' || base === 'skip'\n                        ? '---'\n                        : `${Math.floor(\n                            (score.total / (total || score.total || 1)) * 100,\n                          )}%`}\n                    </td>\n                    <td>\n                      {strands['-1'] ? `${strands['-1']}(-)` : ''}\n                      {strands['1'] ? `${strands['1']}(+)` : ''}\n                    </td>\n                    <td>{key}</td>\n                  </tr>\n                )\n              })\n            })}\n          </tbody>\n        </table>\n      </div>\n    )\n  },\n)\n\ntype Coord = [number, number]\n\nconst SNPCoverageTooltip = observer(\n  (props: {\n    model: any\n    height: number\n    offsetMouseCoord: Coord\n    clientMouseCoord: Coord\n    clientRect?: DOMRect\n  }) => {\n    const { model } = props\n    const { featureUnderMouse: feat } = model\n    return feat && feat.get('type') === 'skip' ? null : (\n      <Tooltip TooltipContents={TooltipContents} {...props} />\n    )\n  },\n)\n\nexport default SNPCoverageTooltip\n","import { BlockSet } from '@jbrowse/core/util/blockTypes'\n\nimport { getSession } from '@jbrowse/core/util'\nimport { getRpcSessionId } from '@jbrowse/core/util/tracks'\nimport { IAnyStateTreeNode } from 'mobx-state-tree'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'\n\nexport async function getUniqueTagValues(\n  self: IAnyStateTreeNode & { adapterConfig: AnyConfigurationModel },\n  colorScheme: { type: string; tag?: string },\n  blocks: BlockSet,\n  opts?: {\n    headers?: Record<string, string>\n    signal?: AbortSignal\n    filters?: string[]\n  },\n) {\n  const { rpcManager } = getSession(self)\n  const { adapterConfig } = self\n  const sessionId = getRpcSessionId(self)\n  const values = await rpcManager.call(\n    getRpcSessionId(self),\n    'PileupGetGlobalValueForTag',\n    {\n      adapterConfig,\n      tag: colorScheme.tag,\n      sessionId,\n      regions: blocks.contentBlocks,\n      ...opts,\n    },\n  )\n  return values as string[]\n}\n\nexport async function getUniqueModificationValues(\n  self: IAnyStateTreeNode & {\n    parentTrack: IAnyStateTreeNode & { configuration: AnyConfigurationModel }\n  },\n  adapterConfig: AnyConfigurationModel,\n  colorScheme: { type: string; tag?: string },\n  blocks: BlockSet,\n  opts?: {\n    headers?: Record<string, string>\n    signal?: AbortSignal\n    filters?: string[]\n  },\n) {\n  const { rpcManager } = getSession(self)\n  const sessionId = getRpcSessionId(self)\n  const values = await rpcManager.call(\n    sessionId,\n    'PileupGetVisibleModifications',\n    {\n      adapterConfig,\n      tag: colorScheme.tag,\n      sessionId,\n      regions: blocks.contentBlocks,\n      ...opts,\n    },\n  )\n  return values as string[]\n}\n","import { addDisposer, types, cast, getEnv, getSnapshot } from 'mobx-state-tree'\nimport { observable, autorun } from 'mobx'\nimport { getConf, readConfObject } from '@jbrowse/core/configuration'\nimport { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle'\nimport {\n  AnyConfigurationSchemaType,\n  AnyConfigurationModel,\n} from '@jbrowse/core/configuration/configurationSchema'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'\nimport { getContainingView } from '@jbrowse/core/util'\nimport Tooltip from '../components/Tooltip'\nimport { getUniqueModificationValues } from '../../shared'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\n// using a map because it preserves order\nconst rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']])\n\ntype LGV = LinearGenomeViewModel\n\nconst stateModelFactory = (\n  pluginManager: PluginManager,\n  configSchema: AnyConfigurationSchemaType,\n) =>\n  types\n    .compose(\n      'LinearSNPCoverageDisplay',\n      linearWiggleDisplayModelFactory(pluginManager, configSchema),\n      types.model({\n        type: types.literal('LinearSNPCoverageDisplay'),\n        drawInterbaseCounts: types.maybe(types.boolean),\n        drawIndicators: types.maybe(types.boolean),\n        drawArcs: types.maybe(types.boolean),\n        filterBy: types.optional(\n          types.model({\n            flagInclude: types.optional(types.number, 0),\n            flagExclude: types.optional(types.number, 1540),\n            readName: types.maybe(types.string),\n            tagFilter: types.maybe(\n              types.model({ tag: types.string, value: types.string }),\n            ),\n          }),\n          {},\n        ),\n        colorBy: types.maybe(\n          types.model({\n            type: types.string,\n            tag: types.maybe(types.string),\n          }),\n        ),\n      }),\n    )\n    .volatile(() => ({\n      modificationTagMap: observable.map({}),\n    }))\n    .actions(self => ({\n      setConfig(configuration: AnyConfigurationModel) {\n        self.configuration = configuration\n      },\n      setFilterBy(filter: {\n        flagInclude: number\n        flagExclude: number\n        readName?: string\n        tagFilter?: { tag: string; value: string }\n      }) {\n        self.filterBy = cast(filter)\n      },\n      setColorBy(colorBy?: { type: string; tag?: string }) {\n        self.colorBy = cast(colorBy)\n      },\n\n      updateModificationColorMap(uniqueModifications: string[]) {\n        const colorPalette = ['red', 'blue', 'green', 'orange', 'purple']\n        let i = 0\n\n        uniqueModifications.forEach(value => {\n          if (!self.modificationTagMap.has(value)) {\n            const newColor = colorPalette[i++]\n            self.modificationTagMap.set(value, newColor)\n          }\n        })\n      },\n    }))\n    .views(self => {\n      const { renderProps: superRenderProps } = self\n      return {\n        get rendererConfig() {\n          const configBlob =\n            getConf(self, ['renderers', self.rendererTypeName]) || {}\n\n          return self.rendererType.configSchema.create(\n            {\n              ...configBlob,\n              drawInterbaseCounts:\n                self.drawInterbaseCounts === undefined\n                  ? configBlob.drawInterbaseCounts\n                  : self.drawInterbaseCounts,\n              drawIndicators:\n                self.drawIndicators === undefined\n                  ? configBlob.drawIndicators\n                  : self.drawIndicators,\n              drawArcs:\n                self.drawArcs === undefined\n                  ? configBlob.drawArcs\n                  : self.drawArcs,\n            },\n            getEnv(self),\n          )\n        },\n        get drawArcsSetting() {\n          return self.drawArcs !== undefined\n            ? self.drawArcs\n            : readConfObject(this.rendererConfig, 'drawArcs')\n        },\n        get drawInterbaseCountsSetting() {\n          return self.drawInterbaseCounts !== undefined\n            ? self.drawInterbaseCounts\n            : readConfObject(this.rendererConfig, 'drawInterbaseCounts')\n        },\n        get drawIndicatorsSetting() {\n          return self.drawIndicators !== undefined\n            ? self.drawIndicators\n            : readConfObject(this.rendererConfig, 'drawIndicators')\n        },\n\n        get modificationsReady() {\n          return self.colorBy?.type === 'modifications'\n            ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap)))\n                .length > 0\n            : true\n        },\n\n        renderProps() {\n          const superProps = superRenderProps()\n          return {\n            ...superProps,\n            notReady: superProps.notReady || !this.modificationsReady,\n            filters: self.filters,\n            modificationTagMap: JSON.parse(\n              JSON.stringify(self.modificationTagMap),\n            ),\n\n            // must use getSnapshot because otherwise changes to e.g. just the\n            // colorBy.type are not read\n            colorBy: self.colorBy ? getSnapshot(self.colorBy) : undefined,\n          }\n        },\n      }\n    })\n    .actions(self => ({\n      toggleDrawIndicators() {\n        self.drawIndicators = !self.drawIndicatorsSetting\n      },\n      toggleDrawInterbaseCounts() {\n        self.drawInterbaseCounts = !self.drawInterbaseCountsSetting\n      },\n      toggleDrawArcs() {\n        self.drawArcs = !self.drawArcsSetting\n      },\n      afterAttach() {\n        addDisposer(\n          self,\n          autorun(\n            async () => {\n              try {\n                const { colorBy } = self\n                const { staticBlocks } = getContainingView(self) as LGV\n                if (colorBy?.type === 'modifications') {\n                  const vals = await getUniqueModificationValues(\n                    self,\n                    getConf(self.parentTrack, 'adapter'),\n                    colorBy,\n                    staticBlocks,\n                  )\n                  self.updateModificationColorMap(vals)\n                }\n              } catch (error) {\n                console.error(error)\n                self.setError(error)\n              }\n            },\n            { delay: 1000 },\n          ),\n        )\n      },\n    }))\n\n    .views(self => {\n      const { trackMenuItems: superTrackMenuItems } = self\n      return {\n        get TooltipComponent() {\n          return Tooltip\n        },\n\n        get adapterConfig() {\n          const subadapter = getConf(self.parentTrack, 'adapter')\n          return {\n            type: 'SNPCoverageAdapter',\n            subadapter,\n          }\n        },\n\n        get rendererTypeName() {\n          return rendererTypes.get('snpcoverage')\n        },\n\n        get needsScalebar() {\n          return true\n        },\n\n        contextMenuItems() {\n          return []\n        },\n\n        trackMenuItems() {\n          return [\n            ...superTrackMenuItems(),\n            {\n              label: 'Draw insertion/clipping indicators',\n              type: 'checkbox',\n              checked: self.drawIndicatorsSetting,\n              onClick: () => {\n                self.toggleDrawIndicators()\n              },\n            },\n            {\n              label: 'Draw insertion/clipping counts',\n              type: 'checkbox',\n              checked: self.drawInterbaseCountsSetting,\n              onClick: () => {\n                self.toggleDrawInterbaseCounts()\n              },\n            },\n            {\n              label: 'Draw arcs',\n              type: 'checkbox',\n              checked: self.drawArcsSetting,\n              onClick: () => {\n                self.toggleDrawArcs()\n              },\n            },\n          ]\n        },\n        // The SNPCoverage filters are called twice because the BAM/CRAM\n        // features pass filters and then the SNPCoverage score features pass\n        // through here, and are already have 'snpinfo' are passed through\n        get filters() {\n          let filters: string[] = []\n          if (self.filterBy) {\n            const { flagInclude, flagExclude, tagFilter, readName } =\n              self.filterBy\n            filters = [\n              `jexl:get(feature,'snpinfo') != undefined ? true : ` +\n                `((get(feature,'flags')&${flagInclude})==${flagInclude}) && ` +\n                `!((get(feature,'flags')&${flagExclude}))`,\n            ]\n\n            if (tagFilter) {\n              const { tag, value } = tagFilter\n              filters.push(\n                `jexl:get(feature,'snpinfo') != undefined ? true : ` +\n                  `\"${value}\" =='*' ? getTag(feature,\"${tag}\") != undefined : ` +\n                  `getTag(feature,\"${tag}\") == \"${value}\"`,\n              )\n            }\n            if (readName) {\n              filters.push(\n                `jexl:get(feature,'snpinfo') != undefined ? true : ` +\n                  `get(feature,'name') == \"${readName}\"`,\n              )\n            }\n          }\n          return new SerializableFilterChain({ filters })\n        },\n      }\n    })\n\nexport type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>\n\nexport default stateModelFactory\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport configSchemaFactory from './models/configSchema'\nimport modelFactory from './models/model'\nimport { LinearWiggleDisplayReactComponent } from '@jbrowse/plugin-wiggle'\nimport DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\n\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addDisplayType(() => {\n    const configSchema = configSchemaFactory(pluginManager)\n    return new DisplayType({\n      name: 'LinearSNPCoverageDisplay',\n      configSchema,\n      stateModel: modelFactory(pluginManager, configSchema),\n      trackType: 'AlignmentsTrack',\n      viewType: 'LinearGenomeView',\n      ReactComponent: LinearWiggleDisplayReactComponent,\n    })\n  })\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view'\nimport { types, Instance } from 'mobx-state-tree'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nfunction PileupConfigFactory(pluginManager: PluginManager) {\n  const PileupRendererConfigSchema =\n    pluginManager.getRendererType('PileupRenderer').configSchema\n  const SvgFeatureRendererConfigSchema =\n    pluginManager.getRendererType('SvgFeatureRenderer').configSchema\n\n  // modify config schema to take in a sub coverage display\n  return ConfigurationSchema(\n    'LinearPileupDisplay',\n    {\n      defaultRendering: {\n        type: 'stringEnum',\n        model: types.enumeration('Rendering', ['pileup', 'svg']),\n        defaultValue: 'pileup',\n      },\n      renderers: ConfigurationSchema('RenderersConfiguration', {\n        PileupRenderer: PileupRendererConfigSchema,\n        SvgFeatureRenderer: SvgFeatureRendererConfigSchema,\n      }),\n      renderer: '',\n      maxFeatureScreenDensity: {\n        type: 'number',\n        description: 'maximum features per pixel that is displayed in the view',\n        defaultValue: 5,\n      },\n      colorScheme: {\n        type: 'stringEnum',\n        model: types.enumeration('colorScheme', [\n          'strand',\n          'normal',\n          'insertSize',\n          'insertSizeAndOrientation',\n          'mappingQuality',\n          'tag',\n        ]),\n        description: 'color scheme to use',\n        defaultValue: 'normal',\n      },\n    },\n    {\n      baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),\n      explicitlyTyped: true,\n    },\n  )\n}\n\nexport type LinearPileupDisplayConfigModel = ReturnType<\n  typeof PileupConfigFactory\n>\nexport type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>\nexport default PileupConfigFactory\n","import React from 'react'\nimport { observer } from 'mobx-react'\nimport Typography from '@material-ui/core/Typography'\n\nexport interface LinearPileupDisplayBlurbProps {\n  model: {\n    sortedBy?: {\n      pos: number\n      refName: number\n      type: string\n    }\n  }\n}\n\nfunction LinearPileupDisplayBlurb(props: LinearPileupDisplayBlurbProps) {\n  const { model } = props\n  const { sortedBy } = model\n  return sortedBy ? (\n    <div\n      data-testid={`blurb-${model.sortedBy}`}\n      style={{ backgroundColor: 'white' }}\n    >\n      <Typography color=\"secondary\" variant=\"caption\">\n        {model.sortedBy\n          ? `Sorted by ${sortedBy.type.toLowerCase()} at ${sortedBy.refName}:${\n              sortedBy.pos\n            }`\n          : null}\n      </Typography>\n    </div>\n  ) : null\n}\nexport default observer(LinearPileupDisplayBlurb)\n","import { lazy } from 'react'\nimport {\n  ConfigurationReference,\n  readConfObject,\n  getConf,\n} from '@jbrowse/core/configuration'\nimport { getRpcSessionId } from '@jbrowse/core/util/tracks'\nimport {\n  getSession,\n  isSessionModelWithWidgets,\n  getContainingView,\n} from '@jbrowse/core/util'\n\nimport VisibilityIcon from '@material-ui/icons/Visibility'\nimport { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons'\nimport {\n  LinearGenomeViewModel,\n  BaseLinearDisplay,\n} from '@jbrowse/plugin-linear-genome-view'\nimport { cast, types, addDisposer, getEnv, Instance } from 'mobx-state-tree'\nimport copy from 'copy-to-clipboard'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport MenuOpenIcon from '@material-ui/icons/MenuOpen'\nimport SortIcon from '@material-ui/icons/Sort'\nimport PaletteIcon from '@material-ui/icons/Palette'\nimport FilterListIcon from '@material-ui/icons/ClearAll'\n\nimport { autorun, observable } from 'mobx'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'\nimport SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'\nimport { LinearPileupDisplayConfigModel } from './configSchema'\nimport LinearPileupDisplayBlurb from './components/LinearPileupDisplayBlurb'\n\nimport { getUniqueTagValues, getUniqueModificationValues } from '../shared'\n\nconst ColorByTagDlg = lazy(() => import('./components/ColorByTag'))\nconst FilterByTagDlg = lazy(() => import('./components/FilterByTag'))\nconst SortByTagDlg = lazy(() => import('./components/SortByTag'))\nconst SetFeatureHeightDlg = lazy(() => import('./components/SetFeatureHeight'))\nconst SetMaxHeightDlg = lazy(() => import('./components/SetMaxHeight'))\nconst ModificationsDlg = lazy(() => import('./components/ColorByModifications'))\n\n// using a map because it preserves order\nconst rendererTypes = new Map([\n  ['pileup', 'PileupRenderer'],\n  ['svg', 'SvgFeatureRenderer'],\n])\n\ntype LGV = LinearGenomeViewModel\n\nconst stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>\n  types\n    .compose(\n      'LinearPileupDisplay',\n      BaseLinearDisplay,\n      types.model({\n        type: types.literal('LinearPileupDisplay'),\n        configuration: ConfigurationReference(configSchema),\n        showSoftClipping: false,\n        featureHeight: types.maybe(types.number),\n        noSpacing: types.maybe(types.boolean),\n        fadeLikelihood: types.maybe(types.boolean),\n        trackMaxHeight: types.maybe(types.number),\n        mismatchAlpha: types.maybe(types.boolean),\n        sortedBy: types.maybe(\n          types.model({\n            type: types.string,\n            pos: types.number,\n            tag: types.maybe(types.string),\n            refName: types.string,\n            assemblyName: types.string,\n          }),\n        ),\n        colorBy: types.maybe(\n          types.model({\n            type: types.string,\n            tag: types.maybe(types.string),\n            extra: types.frozen(),\n          }),\n        ),\n        filterBy: types.optional(\n          types.model({\n            flagInclude: types.optional(types.number, 0),\n            flagExclude: types.optional(types.number, 1540),\n            readName: types.maybe(types.string),\n            tagFilter: types.maybe(\n              types.model({ tag: types.string, value: types.string }),\n            ),\n          }),\n          {},\n        ),\n      }),\n    )\n    .volatile(() => ({\n      colorTagMap: observable.map<string, string>({}),\n      modificationTagMap: observable.map<string, string>({}),\n      ready: false,\n    }))\n    .actions(self => ({\n      setReady(flag: boolean) {\n        self.ready = flag\n      },\n      setMaxHeight(n: number) {\n        self.trackMaxHeight = n\n      },\n      setFeatureHeight(n: number) {\n        self.featureHeight = n\n      },\n      setNoSpacing(flag: boolean) {\n        self.noSpacing = flag\n      },\n\n      setColorScheme(colorScheme: { type: string; tag?: string }) {\n        self.colorTagMap = observable.map({}) // clear existing mapping\n        self.colorBy = cast(colorScheme)\n        self.ready = false\n      },\n\n      updateModificationColorMap(uniqueModifications: string[]) {\n        const colorPalette = ['red', 'blue', 'green', 'orange', 'purple']\n        uniqueModifications.forEach(value => {\n          if (!self.modificationTagMap.has(value)) {\n            const totalKeys = [...self.modificationTagMap.keys()].length\n            const newColor = colorPalette[totalKeys]\n            self.modificationTagMap.set(value, newColor)\n          }\n        })\n      },\n\n      updateColorTagMap(uniqueTag: string[]) {\n        // pale color scheme https://cran.r-project.org/web/packages/khroma/vignettes/tol.html e.g. \"tol_light\"\n        const colorPalette = [\n          '#BBCCEE',\n          'pink',\n          '#CCDDAA',\n          '#EEEEBB',\n          '#FFCCCC',\n          'lightblue',\n          'lightgreen',\n          'tan',\n          '#CCEEFF',\n          'lightsalmon',\n        ]\n\n        uniqueTag.forEach(value => {\n          if (!self.colorTagMap.has(value)) {\n            const totalKeys = [...self.colorTagMap.keys()].length\n            const newColor = colorPalette[totalKeys]\n            self.colorTagMap.set(value, newColor)\n          }\n        })\n      },\n    }))\n    .actions(self => ({\n      afterAttach() {\n        addDisposer(\n          self,\n          autorun(\n            async () => {\n              try {\n                const { rpcManager } = getSession(self)\n                const { sortedBy, colorBy } = self\n                const view = getContainingView(self) as LGV\n\n                // continually generate the vc pairing, set and rerender if any\n                // new values seen\n                if (colorBy?.tag) {\n                  const uniqueTagSet = await getUniqueTagValues(\n                    self,\n                    colorBy,\n                    view.staticBlocks,\n                  )\n                  self.updateColorTagMap(uniqueTagSet)\n                }\n\n                if (colorBy?.type === 'modifications') {\n                  const uniqueModificationsSet =\n                    await getUniqueModificationValues(\n                      self,\n                      getConf(self.parentTrack, ['adapter']),\n                      colorBy,\n                      view.staticBlocks,\n                    )\n                  self.updateModificationColorMap(uniqueModificationsSet)\n                }\n\n                if (sortedBy) {\n                  const { pos, refName, assemblyName } = sortedBy\n\n                  const region = {\n                    start: pos,\n                    end: pos + 1,\n                    refName,\n                    assemblyName,\n                  }\n\n                  // render just the sorted region first\n                  await self.rendererType.renderInClient(rpcManager, {\n                    assemblyName,\n                    regions: [region],\n                    adapterConfig: self.adapterConfig,\n                    rendererType: self.rendererType.name,\n                    sessionId: getRpcSessionId(self),\n                    timeout: 1000000,\n                    ...self.renderProps(),\n                  })\n                  self.setReady(true)\n                  self.setCurrBpPerPx(view.bpPerPx)\n                } else {\n                  self.setReady(true)\n                }\n              } catch (e) {\n                console.error(e)\n                self.setError(e)\n              }\n            },\n            { delay: 1000 },\n          ),\n        )\n      },\n      selectFeature(feature: Feature) {\n        const session = getSession(self)\n        if (isSessionModelWithWidgets(session)) {\n          const featureWidget = session.addWidget(\n            'AlignmentsFeatureWidget',\n            'alignmentFeature',\n            { featureData: feature.toJSON(), view: getContainingView(self) },\n          )\n          session.showWidget(featureWidget)\n        }\n        session.setSelection(feature)\n      },\n\n      clearSelected() {\n        self.sortedBy = undefined\n      },\n\n      // uses copy-to-clipboard and generates notification\n      copyFeatureToClipboard(feature: Feature) {\n        const { uniqueId, ...rest } = feature.toJSON()\n        const session = getSession(self)\n        copy(JSON.stringify(rest, null, 4))\n        session.notify('Copied to clipboard', 'success')\n      },\n\n      toggleSoftClipping() {\n        self.showSoftClipping = !self.showSoftClipping\n      },\n      toggleMismatchAlpha() {\n        self.mismatchAlpha = !self.mismatchAlpha\n      },\n\n      setConfig(configuration: AnyConfigurationModel) {\n        self.configuration = configuration\n      },\n\n      setSortedBy(type: string, tag?: string) {\n        const { centerLineInfo } = getContainingView(self) as LGV\n        if (!centerLineInfo) {\n          return\n        }\n        const { refName, assemblyName, offset } = centerLineInfo\n        const centerBp = Math.round(offset) + 1\n        const centerRefName = refName\n\n        if (centerBp < 0) {\n          return\n        }\n\n        self.sortedBy = {\n          type,\n          pos: centerBp,\n          refName: centerRefName,\n          assemblyName,\n          tag,\n        }\n        self.ready = false\n      },\n      setFilterBy(filter: {\n        flagInclude: number\n        flagExclude: number\n        readName?: string\n        tagFilter?: { tag: string; value: string }\n      }) {\n        self.filterBy = cast(filter)\n      },\n    }))\n    .actions(self => {\n      // resets the sort object and refresh whole display on reload\n      const superReload = self.reload\n\n      return {\n        reload() {\n          self.clearSelected()\n          superReload()\n        },\n      }\n    })\n\n    .views(self => ({\n      get maxHeight() {\n        const conf = getConf(self, ['renderers', self.rendererTypeName]) || {}\n        return self.trackMaxHeight !== undefined\n          ? self.trackMaxHeight\n          : conf.maxHeight\n      },\n      get rendererConfig() {\n        const configBlob =\n          getConf(self, ['renderers', self.rendererTypeName]) || {}\n        return self.rendererType.configSchema.create(\n          {\n            ...configBlob,\n            height: self.featureHeight,\n            noSpacing: self.noSpacing,\n            maxHeight: this.maxHeight,\n            mismatchAlpha: self.mismatchAlpha,\n          },\n          getEnv(self),\n        )\n      },\n      get featureHeightSetting() {\n        return (\n          self.featureHeight || readConfObject(this.rendererConfig, 'height')\n        )\n      },\n      get mismatchAlphaSetting() {\n        return self.mismatchAlpha !== undefined\n          ? self.mismatchAlpha\n          : readConfObject(this.rendererConfig, 'mismatchAlpha')\n      },\n    }))\n    .views(self => {\n      const {\n        trackMenuItems: superTrackMenuItems,\n        renderProps: superRenderProps,\n      } = self\n\n      return {\n        get rendererTypeName() {\n          const viewName = getConf(self, 'defaultRendering')\n          const rendererType = rendererTypes.get(viewName)\n          if (!rendererType) {\n            throw new Error(`unknown alignments view name ${viewName}`)\n          }\n          return rendererType\n        },\n\n        contextMenuItems() {\n          const feat = self.contextMenuFeature\n          const contextMenuItems = feat\n            ? [\n                {\n                  label: 'Open feature details',\n                  icon: MenuOpenIcon,\n                  onClick: () => {\n                    self.clearFeatureSelection()\n                    if (feat) {\n                      self.selectFeature(feat)\n                    }\n                  },\n                },\n                {\n                  label: 'Copy info to clipboard',\n                  icon: ContentCopyIcon,\n                  onClick: () => {\n                    if (feat) {\n                      self.copyFeatureToClipboard(feat)\n                    }\n                  },\n                },\n              ]\n            : []\n          return contextMenuItems\n        },\n\n        get DisplayBlurb() {\n          return LinearPileupDisplayBlurb\n        },\n\n        get filters() {\n          let filters: string[] = []\n          const { flagInclude, flagExclude, tagFilter, readName } =\n            self.filterBy\n\n          filters = [\n            `jexl:((get(feature,'flags')&${flagInclude})==${flagInclude}) && !(get(feature,'flags')&${flagExclude})`,\n          ]\n          if (tagFilter) {\n            const { tag, value } = tagFilter\n            filters.push(\n              `jexl:\"${value}\" =='*' ? getTag(feature,\"${tag}\") != undefined : getTag(feature,\"${tag}\") == \"${value}\"`,\n            )\n          }\n          if (readName) {\n            filters.push(`jexl:get(feature,'name') == \"${readName}\"`)\n          }\n          return new SerializableFilterChain({ filters })\n        },\n\n        renderProps() {\n          const view = getContainingView(self) as LGV\n          const {\n            colorTagMap,\n            modificationTagMap,\n            sortedBy,\n            colorBy,\n            rpcDriverName,\n          } = self\n\n          const superProps = superRenderProps()\n\n          return {\n            ...superProps,\n            notReady:\n              superProps.notReady ||\n              !self.ready ||\n              (sortedBy && self.currBpPerPx !== view.bpPerPx),\n            rpcDriverName,\n            displayModel: self,\n            sortedBy,\n            colorBy,\n            colorTagMap: JSON.parse(JSON.stringify(colorTagMap)),\n            modificationTagMap: JSON.parse(JSON.stringify(modificationTagMap)),\n            filters: this.filters,\n            showSoftClip: self.showSoftClipping,\n            config: self.rendererConfig,\n          }\n        },\n\n        trackMenuItems() {\n          return [\n            ...superTrackMenuItems(),\n            {\n              label: 'Show soft clipping',\n              icon: VisibilityIcon,\n              type: 'checkbox',\n              checked: self.showSoftClipping,\n              onClick: () => {\n                self.toggleSoftClipping()\n                // if toggling from off to on, will break sort for this track\n                // so clear it\n                if (self.showSoftClipping) {\n                  self.clearSelected()\n                }\n              },\n            },\n            {\n              label: 'Sort by',\n              icon: SortIcon,\n              disabled: self.showSoftClipping,\n              subMenu: [\n                ...['Start location', 'Read strand', 'Base pair'].map(\n                  option => {\n                    return {\n                      label: option,\n                      onClick: () => self.setSortedBy(option),\n                    }\n                  },\n                ),\n                {\n                  label: 'Sort by tag...',\n                  onClick: () => {\n                    getSession(self).queueDialog(doneCallback => [\n                      SortByTagDlg,\n                      { model: self, handleClose: doneCallback },\n                    ])\n                  },\n                },\n                {\n                  label: 'Clear sort',\n                  onClick: () => self.clearSelected(),\n                },\n              ],\n            },\n            {\n              label: 'Color scheme',\n              icon: PaletteIcon,\n              subMenu: [\n                {\n                  label: 'Normal',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'normal' })\n                  },\n                },\n                {\n                  label: 'Mapping quality',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'mappingQuality' })\n                  },\n                },\n                {\n                  label: 'Strand',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'strand' })\n                  },\n                },\n                {\n                  label: 'Pair orientation',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'pairOrientation' })\n                  },\n                },\n                {\n                  label: 'Per-base quality',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'perBaseQuality' })\n                  },\n                },\n                {\n                  label: 'Modifications or methylation',\n                  onClick: () => {\n                    getSession(self).queueDialog(doneCallback => [\n                      ModificationsDlg,\n                      { model: self, handleClose: doneCallback },\n                    ])\n                  },\n                },\n                {\n                  label: 'Insert size',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'insertSize' })\n                  },\n                },\n                {\n                  label: 'Stranded paired-end',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'reverseTemplate' })\n                  },\n                },\n                {\n                  label: 'Color by tag...',\n                  onClick: () => {\n                    getSession(self).queueDialog(doneCallback => [\n                      ColorByTagDlg,\n                      { model: self, handleClose: doneCallback },\n                    ])\n                  },\n                },\n              ],\n            },\n            {\n              label: 'Filter by',\n              icon: FilterListIcon,\n              onClick: () => {\n                getSession(self).queueDialog(doneCallback => [\n                  FilterByTagDlg,\n                  { model: self, handleClose: doneCallback },\n                ])\n              },\n            },\n            {\n              label: 'Set feature height',\n              onClick: () => {\n                getSession(self).queueDialog(doneCallback => [\n                  SetFeatureHeightDlg,\n                  { model: self, handleClose: doneCallback },\n                ])\n              },\n            },\n            {\n              label: 'Set max height',\n              onClick: () => {\n                getSession(self).queueDialog(doneCallback => [\n                  SetMaxHeightDlg,\n                  { model: self, handleClose: doneCallback },\n                ])\n              },\n            },\n            {\n              label: 'Fade mismatches by quality',\n              type: 'checkbox',\n              checked: self.mismatchAlphaSetting,\n              onClick: () => {\n                self.toggleMismatchAlpha()\n              },\n            },\n          ]\n        },\n      }\n    })\n\nexport type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>\nexport type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>\n\nexport default stateModelFactory\n","import configSchemaFactory from './configSchema'\nimport modelFactory from './model'\nimport DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'\n\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addDisplayType(() => {\n    const configSchema = configSchemaFactory(pluginManager)\n    return new DisplayType({\n      name: 'LinearPileupDisplay',\n      configSchema,\n      stateModel: modelFactory(configSchema),\n      trackType: 'AlignmentsTrack',\n      viewType: 'LinearGenomeView',\n      ReactComponent: BaseLinearDisplayComponent,\n    })\n  })\n}\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport {\n  createBaseTrackConfig,\n  createBaseTrackModel,\n} from '@jbrowse/core/pluggableElementTypes/models'\nfunction configSchemaFactory(pluginManager: PluginManager) {\n  return ConfigurationSchema(\n    'AlignmentsTrack',\n    {},\n    { baseConfiguration: createBaseTrackConfig(pluginManager) },\n  )\n}\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addTrackType(() => {\n    const configSchema = configSchemaFactory(pluginManager)\n    const track = new TrackType({\n      name: 'AlignmentsTrack',\n      configSchema,\n      stateModel: createBaseTrackModel(\n        pluginManager,\n        'AlignmentsTrack',\n        configSchema,\n      ),\n    })\n    const linearAlignmentsDisplay = pluginManager.getDisplayType(\n      'LinearAlignmentsDisplay',\n    )\n    // Add LinearAlignmentsDisplay here so that it has priority over the other\n    // linear displays (defaults to order the displays are added, but we have\n    // to add the Pileup and SNPCoverage displays first).\n    track.addDisplayType(linearAlignmentsDisplay)\n    return track\n  })\n}\n","import { lazy } from 'react'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { ElementId } from '@jbrowse/core/util/types/mst'\nimport { types } from 'mobx-state-tree'\nimport WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'\n\nconst configSchema = ConfigurationSchema('AlignmentsFeatureWidget', {})\n\nexport function stateModelFactory(pluginManager: PluginManager) {\n  return types\n    .model('AlignmentsFeatureWidget', {\n      id: ElementId,\n      type: types.literal('AlignmentsFeatureWidget'),\n      featureData: types.frozen(),\n      view: types.safeReference(\n        pluginManager.pluggableMstType('view', 'stateModel'),\n      ),\n    })\n    .actions(self => ({\n      setFeatureData(data: unknown) {\n        self.featureData = data\n      },\n      clearFeatureData() {\n        self.featureData = undefined\n      },\n    }))\n}\n\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addWidgetType(\n    () =>\n      new WidgetType({\n        name: 'AlignmentsFeatureWidget',\n        heading: 'Feature details',\n        configSchema,\n        stateModel: stateModelFactory(pluginManager),\n        ReactComponent: lazy(() => import('./AlignmentsFeatureDetail')),\n      }),\n  )\n}\n\nexport { configSchema }\n","import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'\nimport { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'\nimport { renameRegionsIfNeeded } from '@jbrowse/core/util'\nimport { Region } from '@jbrowse/core/util/types'\nimport { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'\nimport { toArray } from 'rxjs/operators'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getTagAlt } from '../util'\nimport { getModificationTypes } from '../BamAdapter/MismatchParser'\n\nexport class PileupGetGlobalValueForTag extends RpcMethodType {\n  name = 'PileupGetGlobalValueForTag'\n\n  async serializeArguments(\n    args: RenderArgs & { signal?: AbortSignal; statusCallback?: Function },\n    rpcDriverClassName: string,\n  ) {\n    const { rootModel } = this.pluginManager\n    const assemblyManager = rootModel?.session?.assemblyManager\n    if (!assemblyManager) {\n      throw new Error('no assembly manager available')\n    }\n\n    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args)\n\n    return super.serializeArguments(renamedArgs, rpcDriverClassName)\n  }\n\n  async execute(\n    args: {\n      adapterConfig: {}\n      signal?: RemoteAbortSignal\n      headers?: Record<string, string>\n      regions: Region[]\n      sessionId: string\n      tag: string\n    },\n    rpcDriverClassName: string,\n  ) {\n    const deserializedArgs = await this.deserializeArguments(\n      args,\n      rpcDriverClassName,\n    )\n    const { adapterConfig, sessionId, regions, tag } = deserializedArgs\n    const dataAdapter = (\n      await getAdapter(this.pluginManager, sessionId, adapterConfig)\n    ).dataAdapter as BaseFeatureDataAdapter\n\n    const features = dataAdapter.getFeaturesInMultipleRegions(regions)\n    const featuresArray = await features.pipe(toArray()).toPromise()\n    const uniqueValues = new Set<string>()\n    featuresArray.forEach(feature => {\n      const tags = feature.get('tags')\n      const val = tags ? tags[tag] : feature.get(tag)\n      if (val !== undefined) {\n        uniqueValues.add(`${val}`)\n      }\n    })\n    return [...uniqueValues]\n  }\n}\n\nexport class PileupGetVisibleModifications extends RpcMethodType {\n  name = 'PileupGetVisibleModifications'\n\n  async serializeArguments(\n    args: RenderArgs & { signal?: AbortSignal; statusCallback?: Function },\n    rpcDriverClassName: string,\n  ) {\n    const { rootModel } = this.pluginManager\n    const assemblyManager = rootModel?.session?.assemblyManager\n    if (!assemblyManager) {\n      throw new Error('no assembly manager available')\n    }\n\n    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args)\n\n    return super.serializeArguments(renamedArgs, rpcDriverClassName)\n  }\n\n  async execute(\n    args: {\n      adapterConfig: {}\n      signal?: RemoteAbortSignal\n      headers?: Record<string, string>\n      regions: Region[]\n      sessionId: string\n      tag: string\n    },\n    rpcDriverClassName: string,\n  ) {\n    const deserializedArgs = await this.deserializeArguments(\n      args,\n      rpcDriverClassName,\n    )\n    const { adapterConfig, sessionId, regions } = deserializedArgs\n    const dataAdapter = (\n      await getAdapter(this.pluginManager, sessionId, adapterConfig)\n    ).dataAdapter as BaseFeatureDataAdapter\n\n    const features = dataAdapter.getFeaturesInMultipleRegions(regions)\n    const featuresArray = await features.pipe(toArray()).toPromise()\n    const uniqueValues = new Set<string>()\n    featuresArray.forEach(feature => {\n      const val = (getTagAlt(feature, 'MM', 'Mm') as string) || ''\n      if (val !== undefined) {\n        getModificationTypes(val).forEach(t => uniqueValues.add(t))\n      }\n    })\n    return [...uniqueValues]\n  }\n}\n","import { FileLocation } from '@jbrowse/core/util/types'\nimport Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport * as MismatchParser from './BamAdapter/MismatchParser'\nimport { LinearPileupDisplayModel } from './LinearPileupDisplay/model'\n\nimport BamAdapterF from './CramAdapter'\nimport CramAdapterF from './BamAdapter'\nimport HtsgetBamAdapterF from './HtsgetBamAdapter'\nimport SNPCoverageAdapterF from './SNPCoverageAdapter'\nimport SNPCoverageRendererF from './SNPCoverageRenderer'\nimport PileupRendererF from './PileupRenderer'\nimport LinearAlignmentsDisplayF from './LinearAlignmentsDisplay'\nimport LinearSNPCoverageDisplayF from './LinearSNPCoverageDisplay'\nimport LinearPileupDisplayF from './LinearPileupDisplay'\nimport AlignmentsTrackF from './AlignmentsTrack'\nimport AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail'\n\nimport {\n  PileupGetGlobalValueForTag,\n  PileupGetVisibleModifications,\n} from './PileupRPC/rpcMethods'\nimport {\n  makeIndex,\n  makeIndexType,\n  getFileName,\n  AdapterGuesser,\n  TrackTypeGuesser,\n} from '@jbrowse/core/util/tracks'\n\nexport { MismatchParser }\nexport type { LinearPileupDisplayModel }\n\nexport default class AlignmentsPlugin extends Plugin {\n  name = 'AlignmentsPlugin'\n\n  install(pluginManager: PluginManager) {\n    ;[\n      CramAdapterF,\n      BamAdapterF,\n      LinearPileupDisplayF,\n      LinearSNPCoverageDisplayF,\n      AlignmentsTrackF,\n      SNPCoverageAdapterF,\n      HtsgetBamAdapterF,\n      PileupRendererF,\n      SNPCoverageRendererF,\n      LinearAlignmentsDisplayF,\n      AlignmentsFeatureWidgetF,\n    ].map(f => f(pluginManager))\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 = /\\.cram$/i\n          const adapterName = 'CramAdapter'\n          const fileName = getFileName(file)\n          const obj = {\n            type: adapterName,\n            cramLocation: file,\n            craiLocation: index || makeIndex(file, '.crai'),\n          }\n          if (regexGuess.test(fileName) && !adapterHint) {\n            return obj\n          } else if (adapterHint === adapterName) {\n            return obj\n          }\n          return adapterGuesser(file, index, adapterHint)\n        }\n      },\n    )\n\n    pluginManager.addToExtensionPoint(\n      'Core-guessAdapterForLocation',\n      (adapterGuesser: AdapterGuesser) => {\n        return (\n          file: FileLocation,\n          index?: FileLocation,\n          adapterHint?: string,\n        ) => {\n          const regexGuess = /\\.bam$/i\n          const adapterName = 'BamAdapter'\n          const fileName = getFileName(file)\n          const indexName = index && getFileName(index)\n\n          const obj = {\n            type: adapterName,\n            bamLocation: file,\n            index: {\n              location: index || makeIndex(file, '.bai'),\n              indexType: makeIndexType(indexName, 'CSI', 'BAI'),\n            },\n          }\n          if (regexGuess.test(fileName) && !adapterHint) {\n            return obj\n          } else if (adapterHint === adapterName) {\n            return obj\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 === 'BamAdapter' || adapterName === 'CramAdapter') {\n            return 'AlignmentsTrack'\n          }\n          return trackTypeGuesser(adapterName)\n        }\n      },\n    )\n\n    pluginManager.addRpcMethod(\n      () => new PileupGetGlobalValueForTag(pluginManager),\n    )\n    pluginManager.addRpcMethod(\n      () => new PileupGetVisibleModifications(pluginManager),\n    )\n  }\n}\n","/* eslint-disable no-underscore-dangle */\nimport {\n  Feature,\n  SimpleFeatureSerialized,\n} from '@jbrowse/core/util/simpleFeature'\n\nimport CramAdapter from './CramAdapter'\n\nexport interface Mismatch {\n  qual?: number\n  start: number\n  length: number\n  type: string\n  base: string\n  altbase?: string\n  seq?: string\n  cliplen?: number\n}\n\nexport default class CramSlightlyLazyFeature implements Feature {\n  private _store: CramAdapter\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  constructor(private record: any, store: CramAdapter) {\n    this._store = store\n  }\n\n  _get_name() {\n    return this.record.readName\n  }\n\n  _get_start() {\n    return this.record.alignmentStart - 1\n  }\n\n  _get_end() {\n    return this.record.alignmentStart + this.record.lengthOnRef - 1\n  }\n\n  _get_cram_read_features() {\n    return this.record.readFeatures\n  }\n\n  _get_type() {\n    return 'match'\n  }\n\n  _get_score() {\n    return this.record.mappingQuality\n  }\n\n  _get_flags() {\n    return this.record.flags\n  }\n\n  _get_strand() {\n    return this.record.isReverseComplemented() ? -1 : 1\n  }\n\n  _read_group_id() {\n    const rg = this._store.samHeader.readGroups\n    return rg ? rg[this.record.readGroupId] : undefined\n  }\n\n  _get_qual() {\n    return (this.record.qualityScores || []).join(' ')\n  }\n\n  qualRaw() {\n    return this.record.qualityScores\n  }\n\n  _get_seq_id() {\n    return this._store.refIdToName(this.record.sequenceId)\n  }\n\n  _get_refName() {\n    return this._get_seq_id()\n  }\n\n  _get_is_paired() {\n    return !!this.record.mate\n  }\n\n  _get_pair_orientation() {\n    return this.record.isPaired() ? this.record.getPairOrientation() : undefined\n  }\n\n  _get_template_length() {\n    return this.record.templateLength || this.record.templateSize\n  }\n\n  _get_next_seq_id() {\n    return this.record.mate\n      ? this._store.refIdToName(this.record.mate.sequenceId)\n      : undefined\n  }\n\n  _get_next_pos() {\n    return this.record.mate ? this.record.mate.alignmentStart : undefined\n  }\n\n  _get_next_segment_position() {\n    return this.record.mate\n      ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${\n          this.record.mate.alignmentStart\n        }`\n      : undefined\n  }\n\n  _get_tags() {\n    const RG = this._read_group_id()\n    const { tags } = this.record\n    // avoids a tag copy if no RG, but just copy if there is one\n    return RG !== undefined ? { ...tags, RG } : tags\n  }\n\n  _get_seq() {\n    return this.record.getReadBases()\n  }\n\n  // generate a CIGAR, based on code from jkbonfield\n  _get_CIGAR() {\n    let seq = ''\n    let cigar = ''\n    let op = 'M'\n    let oplen = 0\n\n    // not sure I should access these, but...\n    const ref = this.record._refRegion.seq\n    const refStart = this.record._refRegion.start\n    let last_pos = this.record.alignmentStart\n    let sublen = 0\n    if (typeof this.record.readFeatures !== 'undefined') {\n      // @ts-ignore\n      this.record.readFeatures.forEach(({ code, refPos, sub, data }) => {\n        sublen = refPos - last_pos\n        seq += ref.substring(last_pos - refStart, refPos - refStart)\n        last_pos = refPos\n\n        if (oplen && op !== 'M') {\n          cigar += oplen + op\n          oplen = 0\n        }\n        if (sublen) {\n          op = 'M'\n          oplen += sublen\n        }\n\n        if (code === 'b') {\n          // An array of bases stored verbatim\n          const ret = data.split(',')\n          const added = String.fromCharCode(...ret)\n          seq += added\n          last_pos += added.length\n          oplen += added.length\n        } else if (code === 'B') {\n          // Single base (+ qual score)\n          seq += sub\n          last_pos++\n          oplen++\n        } else if (code === 'X') {\n          // Substitution\n          seq += sub\n          last_pos++\n          oplen++\n        } else if (code === 'D' || code === 'N') {\n          // Deletion or Ref Skip\n          last_pos += data\n          if (oplen) {\n            cigar += oplen + op\n          }\n          cigar += data + code\n          oplen = 0\n        } else if (code === 'I' || code === 'S') {\n          // Insertion or soft-clip\n          seq += data\n          if (oplen) {\n            cigar += oplen + op\n          }\n          cigar += data.length + code\n          oplen = 0\n        } else if (code === 'i') {\n          // Single base insertion\n          seq += data\n          if (oplen) {\n            cigar += oplen + op\n          }\n          cigar += `${1}I`\n          oplen = 0\n        } else if (code === 'P') {\n          // Padding\n          if (oplen) {\n            cigar += oplen + op\n          }\n          cigar += `${data}P`\n        } else if (code === 'H') {\n          // Hard clip\n          if (oplen) {\n            cigar += oplen + op\n          }\n          cigar += `${data}H`\n          oplen = 0\n        } // else q or Q\n      })\n    } else {\n      sublen = this.record.readLength - seq.length\n    }\n    if (seq.length !== this.record.readLength) {\n      sublen = this.record.readLength - seq.length\n      seq += ref.substring(last_pos - refStart, last_pos - refStart + sublen)\n\n      if (oplen && op !== 'M') {\n        cigar += oplen + op\n        oplen = 0\n      }\n      op = 'M'\n      oplen += sublen\n    }\n    if (oplen) {\n      cigar += oplen + op\n    }\n    return cigar\n  }\n\n  tags() {\n    const properties = Object.getOwnPropertyNames(\n      CramSlightlyLazyFeature.prototype,\n    )\n    return properties\n      .filter(\n        prop =>\n          prop.startsWith('_get_') &&\n          prop !== '_get_mismatches' &&\n          prop !== '_get_skips_and_dels' &&\n          prop !== '_get_cram_read_features',\n      )\n      .map(methodName => methodName.replace('_get_', ''))\n  }\n\n  id() {\n    return `${this._store.id}-${this.record.uniqueId}`\n  }\n\n  get(field: string) {\n    const methodName = `_get_${field}`\n    // @ts-ignore\n    if (this[methodName]) {\n      // @ts-ignore\n      return this[methodName]()\n    }\n    return undefined\n  }\n\n  parent(): undefined | Feature {\n    return undefined\n  }\n\n  children(): undefined | Feature[] {\n    return undefined\n  }\n\n  set(): void {}\n\n  pairedFeature() {\n    return false\n  }\n\n  _get_clipPos() {\n    const mismatches = this.get('mismatches')\n    if (mismatches.length) {\n      const record =\n        this.get('strand') === -1\n          ? mismatches[mismatches.length - 1]\n          : mismatches[0]\n      const { type, cliplen } = record\n      if (type === 'softclip' || type === 'hardclip') {\n        return cliplen\n      }\n    }\n    return 0\n  }\n\n  toJSON(): SimpleFeatureSerialized {\n    // eslint-disable-next-line @typescript-eslint/no-explicit-any\n    const tags: Record<string, any> = {}\n    this.tags().forEach((t: string) => {\n      const val = this.get(t)\n      if (val !== undefined) {\n        tags[t] = val\n      }\n    })\n\n    return {\n      ...tags,\n      name: this.get('name'),\n      type: this.get('type'),\n      uniqueId: this.id(),\n    }\n  }\n\n  _get_mismatches(): Mismatch[] {\n    const readFeatures = this.get('cram_read_features')\n    const qual = this.qualRaw()\n    if (!readFeatures) {\n      return []\n    }\n    const start = this.get('start')\n    const mismatches: Mismatch[] = []\n    readFeatures.forEach(\n      (args: {\n        code: string\n        refPos: number\n        // eslint-disable-next-line @typescript-eslint/no-explicit-any\n        data: any\n        pos: number\n        sub: string\n        ref: string\n      }) => {\n        const { code, pos, data, sub, ref } = args\n        const refPos = args.refPos - 1 - start\n        if (code === 'X') {\n          // substitution\n          mismatches.push({\n            start: refPos,\n            length: 1,\n            base: sub,\n            qual: qual?.[pos],\n            altbase: ref,\n            type: 'mismatch',\n          })\n        } else if (code === 'I') {\n          // insertion\n          mismatches.push({\n            start: refPos,\n            type: 'insertion',\n            base: `${data.length}`,\n            length: 0,\n          })\n        } else if (code === 'N') {\n          // reference skip\n          mismatches.push({\n            type: 'skip',\n            length: data,\n            start: refPos,\n            base: 'N',\n          })\n        } else if (code === 'S') {\n          // soft clip\n          const len = data.length\n          mismatches.push({\n            start: refPos,\n            type: 'softclip',\n            base: `S${len}`,\n            cliplen: len,\n            length: 1,\n          })\n        } else if (code === 'P') {\n          // padding\n        } else if (code === 'H') {\n          // hard clip\n          const len = data\n          mismatches.push({\n            start: refPos,\n            type: 'hardclip',\n            base: `H${len}`,\n            cliplen: len,\n            length: 1,\n          })\n        } else if (code === 'D') {\n          // deletion\n          mismatches.push({\n            type: 'deletion',\n            length: data,\n            start: refPos,\n            base: '*',\n          })\n        } else if (code === 'b') {\n          // stretch of bases\n        } else if (code === 'q') {\n          // stretch of qual scores\n        } else if (code === 'B') {\n          // a pair of [base, qual]\n        } else if (code === 'i') {\n          // single-base insertion\n          // insertion\n          mismatches.push({\n            start: refPos,\n            type: 'insertion',\n            base: data,\n            length: 1,\n          })\n        } else if (code === 'Q') {\n          // single quality value\n        }\n      },\n    )\n    return mismatches\n  }\n\n  _get_skips_and_dels(): Mismatch[] {\n    return this._get_mismatches()\n  }\n}\n","import { CraiIndex, IndexedCramFile } from '@gmod/cram'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { Region } from '@jbrowse/core/util/types'\nimport { checkAbortSignal } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { toArray } from 'rxjs/operators'\nimport CramSlightlyLazyFeature from './CramSlightlyLazyFeature'\n\ninterface HeaderLine {\n  tag: string\n  value: any // eslint-disable-line @typescript-eslint/no-explicit-any\n  data: HeaderLine[]\n}\ninterface Header {\n  idToName?: string[]\n  nameToId?: Record<string, number>\n  readGroups?: number[]\n}\n\nexport default class CramAdapter extends BaseFeatureDataAdapter {\n  samHeader: Header = {}\n\n  private setupP?: Promise<{\n    samHeader: Header\n    cram: any // eslint-disable-line @typescript-eslint/no-explicit-any\n    sequenceAdapter: any // eslint-disable-line @typescript-eslint/no-explicit-any\n  }>\n\n  // maps a refname to an id\n  private seqIdToRefName: string[] | undefined\n\n  // maps a seqId to original refname, passed specially to render args, to a seqid\n  private seqIdToOriginalRefName: string[] = []\n\n  public async configure() {\n    const cramLocation = readConfObject(this.config, 'cramLocation')\n    const craiLocation = readConfObject(this.config, 'craiLocation')\n    if (!cramLocation) {\n      throw new Error('missing cramLocation argument')\n    }\n    if (!craiLocation) {\n      throw new Error('missing craiLocation argument')\n    }\n\n    // eslint-disable-next-line @typescript-eslint/no-explicit-any\n    const cram: any = new IndexedCramFile({\n      cramFilehandle: openLocation(cramLocation, this.pluginManager),\n      index: new CraiIndex({\n        filehandle: openLocation(craiLocation, this.pluginManager),\n      }),\n      seqFetch: this.seqFetch.bind(this),\n      checkSequenceMD5: false,\n      fetchSizeLimit: 200_000_000, // just make this a large size to avoid hitting it\n    })\n    // instantiate the sequence adapter\n    const sequenceAdapterType = readConfObject(this.config, [\n      'sequenceAdapter',\n      'type',\n    ])\n\n    if (!this.getSubAdapter) {\n      throw new Error('Error getting subadapter')\n    }\n\n    const seqConf = readConfObject(this.config, 'sequenceAdapter')\n    const { dataAdapter: sequenceAdapter } = await this.getSubAdapter(seqConf)\n\n    if (!(sequenceAdapter instanceof BaseFeatureDataAdapter)) {\n      throw new Error(\n        `CRAM feature adapters cannot use sequence adapters of type '${sequenceAdapterType}'`,\n      )\n    }\n\n    return { cram, sequenceAdapter }\n  }\n\n  async getHeader(opts?: BaseOptions) {\n    const { cram } = await this.configure()\n    return cram.cram.getHeaderText(opts)\n  }\n\n  private async seqFetch(seqId: number, start: number, end: number) {\n    start -= 1 // convert from 1-based closed to interbase\n\n    const { sequenceAdapter } = await this.configure()\n    const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId)\n    if (!refName) {\n      return undefined\n    }\n\n    const seqChunks = await sequenceAdapter\n      .getFeatures({\n        refName,\n        start,\n        end,\n        assemblyName: '',\n      })\n      .pipe(toArray())\n      .toPromise()\n\n    const sequence = seqChunks\n      .sort((a, b) => a.get('start') - b.get('start'))\n      .map(chunk => {\n        const chunkStart = chunk.get('start')\n        const chunkEnd = chunk.get('end')\n        const trimStart = Math.max(start - chunkStart, 0)\n        const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart)\n        const trimLength = trimEnd - trimStart\n        const chunkSeq = chunk.get('seq') || chunk.get('residues')\n        return chunkSeq.substr(trimStart, trimLength)\n      })\n      .join('')\n\n    if (sequence.length !== end - start) {\n      throw new Error(\n        `sequence fetch failed: fetching ${refName}:${(\n          start - 1\n        ).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(\n          end - start\n        ).toLocaleString()}`,\n      )\n    }\n    return sequence\n  }\n\n  private async setupPre(opts?: BaseOptions) {\n    const { statusCallback = () => {} } = opts || {}\n    const configured = await this.configure()\n    statusCallback('Downloading index')\n    const { cram } = configured\n    const samHeader: HeaderLine[] = await cram.cram.getSamHeader(opts?.signal)\n\n    // use the @SQ lines in the header to figure out the\n    // mapping between ref ID numbers and names\n    const idToName: string[] = []\n    const nameToId: Record<string, number> = {}\n    samHeader\n      .filter(l => l.tag === 'SQ')\n      .forEach((sqLine, refId) => {\n        sqLine.data.forEach(item => {\n          if (item.tag === 'SN') {\n            // this is the ref name\n            const refName = item.value\n            nameToId[refName] = refId\n            idToName[refId] = refName\n          }\n        })\n      })\n\n    const readGroups = samHeader\n      .filter(l => l.tag === 'RG')\n      .map(rgLine => rgLine.data.find(item => item.tag === 'ID')?.value)\n\n    const data = { idToName, nameToId, readGroups }\n    statusCallback('')\n    this.samHeader = data\n    return { samHeader: data, ...configured }\n  }\n\n  private async setup(opts?: BaseOptions) {\n    if (!this.setupP) {\n      this.setupP = this.setupPre(opts).catch(e => {\n        this.setupP = undefined\n        throw e\n      })\n    }\n    return this.setupP\n  }\n\n  async getRefNames(opts?: BaseOptions) {\n    const { samHeader } = await this.setup(opts)\n    if (!samHeader.idToName) {\n      throw new Error('CRAM file has no header lines')\n    }\n    return samHeader.idToName\n  }\n\n  // use info from the SAM header if possible, but fall back to using\n  // the ref seq order from when the browser's refseqs were loaded\n  refNameToId(refName: string) {\n    if (this.samHeader.nameToId) {\n      return this.samHeader.nameToId[refName]\n    }\n    if (this.seqIdToRefName) {\n      return this.seqIdToRefName.indexOf(refName)\n    }\n    return undefined\n  }\n\n  // use info from the SAM header if possible, but fall back to using\n  // the ref seq order from when the browser's refseqs were loaded\n  refIdToName(refId: number) {\n    if (this.samHeader.idToName) {\n      return this.samHeader.idToName[refId]\n    }\n    if (this.seqIdToRefName) {\n      return this.seqIdToRefName[refId]\n    }\n    return undefined\n  }\n\n  refIdToOriginalName(refId: number) {\n    return this.seqIdToOriginalRefName[refId]\n  }\n\n  getFeatures(\n    region: Region & { originalRefName?: string },\n    opts?: BaseOptions,\n  ) {\n    const { signal, statusCallback = () => {} } = opts || {}\n    const { refName, start, end, originalRefName } = region\n\n    return ObservableCreate<Feature>(async observer => {\n      const { cram, sequenceAdapter } = await this.setup(opts)\n      statusCallback('Downloading alignments')\n      if (!this.seqIdToRefName) {\n        this.seqIdToRefName = await sequenceAdapter.getRefNames(opts)\n      }\n      const refId = this.refNameToId(refName)\n      if (refId !== undefined) {\n        if (originalRefName) {\n          this.seqIdToOriginalRefName[refId] = originalRefName\n        }\n        const records = await cram.getRecordsForRange(refId, start, end, opts)\n        checkAbortSignal(signal)\n        // eslint-disable-next-line @typescript-eslint/no-explicit-any\n        records.forEach((record: any) => {\n          observer.next(this.cramRecordToFeature(record))\n        })\n      } else {\n        console.warn('Unknown refName', refName)\n      }\n      statusCallback('')\n      observer.complete()\n    }, signal)\n  }\n\n  freeResources(/* { region } */): void {}\n\n  cramRecordToFeature(record: unknown) {\n    return new CramSlightlyLazyFeature(record, this)\n  }\n\n  // we return the configured fetchSizeLimit, and the bytes for the region\n  async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {\n    const bytes = await this.bytesForRegions(regions, opts)\n    const fetchSizeLimit = readConfObject(this.config, 'fetchSizeLimit')\n    return {\n      bytes,\n      fetchSizeLimit,\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[], _opts?: BaseOptions) {\n    const { cram } = await this.configure()\n    const blockResults = await Promise.all(\n      regions.map(region => {\n        const { refName, start, end } = region\n        const chrId = this.refNameToId(refName)\n        return cram.index.getEntriesForRange(chrId, start, end)\n      }),\n    )\n\n    return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0)\n  }\n}\n","/* eslint-disable no-underscore-dangle */\nimport {\n  Feature,\n  SimpleFeatureSerialized,\n} from '@jbrowse/core/util/simpleFeature'\nimport { BamRecord } from '@gmod/bam'\nimport {\n  parseCigar,\n  generateMD,\n  cigarToMismatches,\n  mdToMismatches,\n  Mismatch,\n} from './MismatchParser'\n\nimport BamAdapter from './BamAdapter'\n\nexport default class BamSlightlyLazyFeature implements Feature {\n  private cachedMD = ''\n  constructor(\n    private record: BamRecord,\n    private adapter: BamAdapter,\n    private ref?: string,\n  ) {}\n\n  _get_name() {\n    return this.record.get('name')\n  }\n\n  _get_type(): string {\n    return 'match'\n  }\n\n  _get_score(): number {\n    return this.record.get('mq')\n  }\n\n  _get_flags(): string {\n    return this.record.flags\n  }\n\n  _get_strand(): number {\n    return this.record.isReverseComplemented() ? -1 : 1\n  }\n\n  _get_pair_orientation() {\n    return this.record.isPaired() ? this.record.getPairOrientation() : undefined\n  }\n\n  _get_next_seq_id() {\n    return this.record._next_refid()\n  }\n\n  _get_seq_id() {\n    // @ts-ignore\n    return this.record._refID\n  }\n\n  _get_next_refName() {\n    return this.adapter.refIdToName(this.record._next_refid())\n  }\n\n  _get_next_segment_position() {\n    const { record, adapter } = this\n    return record.isPaired()\n      ? `${adapter.refIdToName(record._next_refid())}:${record._next_pos() + 1}`\n      : undefined\n  }\n\n  _get_seq() {\n    return this.record.getReadBases()\n  }\n\n  _get_MD() {\n    const md = this.record.get('MD') || this.cachedMD\n    if (!md) {\n      const seq = this.get('seq')\n      if (seq && this.ref) {\n        this.cachedMD = generateMD(this.ref, this.get('seq'), this.get('CIGAR'))\n        return this.cachedMD\n      }\n    }\n    return md\n  }\n\n  qualRaw() {\n    return this.record.qualRaw()\n  }\n\n  set() {}\n\n  tags() {\n    const properties = Object.getOwnPropertyNames(\n      BamSlightlyLazyFeature.prototype,\n    )\n\n    return [\n      ...new Set(\n        properties\n          .filter(\n            prop =>\n              prop.startsWith('_get_') &&\n              prop !== '_get_mismatches' &&\n              prop !== '_get_skips_and_dels' &&\n              prop !== '_get_cram_read_features' &&\n              prop !== '_get_tags' &&\n              prop !== '_get_next_seq_id' &&\n              prop !== '_get_seq_id',\n          )\n          .map(methodName => methodName.replace('_get_', ''))\n          .concat(this.record._tags()),\n      ),\n    ]\n  }\n\n  id() {\n    return `${this.adapter.id}-${this.record.id()}`\n  }\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  get(field: string): any {\n    const methodName = `_get_${field}`\n    // @ts-ignore\n    if (this[methodName]) {\n      // @ts-ignore\n      return this[methodName]()\n    }\n    return this.record.get(field)\n  }\n\n  _get_refName() {\n    return this.adapter.refIdToName(this.record.seq_id())\n  }\n\n  parent() {\n    return undefined\n  }\n\n  children() {\n    return undefined\n  }\n\n  pairedFeature() {\n    return false\n  }\n\n  toJSON(): SimpleFeatureSerialized {\n    return {\n      ...Object.fromEntries(\n        this.tags()\n          .map(t => [t, this.get(t)])\n          .filter(elt => elt[1] !== undefined),\n      ),\n      uniqueId: this.id(),\n    }\n  }\n\n  _get_skips_and_dels(\n    opts: {\n      cigarAttributeName: string\n    } = {\n      cigarAttributeName: 'CIGAR',\n    },\n  ) {\n    const { cigarAttributeName } = opts\n    let mismatches: Mismatch[] = []\n    let cigarOps: string[] = []\n\n    // parse the CIGAR tag if it has one\n    const cigarString = this.get(cigarAttributeName)\n    if (cigarString) {\n      cigarOps = parseCigar(cigarString)\n      mismatches = mismatches.concat(\n        cigarToMismatches(cigarOps, this.get('seq'), this.qualRaw()),\n      )\n    }\n    return mismatches\n  }\n\n  _get_mismatches({\n    cigarAttributeName = 'CIGAR',\n    mdAttributeName = 'MD',\n  }: {\n    cigarAttributeName?: string\n    mdAttributeName?: string\n  } = {}) {\n    let mismatches: Mismatch[] = []\n    let cigarOps: string[] = []\n\n    // parse the CIGAR tag if it has one\n    const cigarString = this.get(cigarAttributeName)\n    const seq = this.get('seq')\n    const qual = this.qualRaw()\n    if (cigarString) {\n      cigarOps = parseCigar(cigarString)\n      mismatches = mismatches.concat(cigarToMismatches(cigarOps, seq, qual))\n    }\n\n    // now let's look for CRAM or MD mismatches\n    const mdString = this.get(mdAttributeName)\n    if (mdString) {\n      mismatches = mismatches.concat(\n        mdToMismatches(mdString, cigarOps, mismatches, seq, qual),\n      )\n    }\n\n    // uniqify the mismatches\n    const seen: { [index: string]: boolean } = {}\n    return mismatches.filter(m => {\n      const key = `${m.type},${m.start},${m.length}`\n      const s = seen[key]\n      seen[key] = true\n      return !s\n    })\n  }\n\n  _get_clipPos() {\n    const cigar = this.get('CIGAR') || ''\n    return this.get('strand') === -1\n      ? +(cigar.match(/(\\d+)[SH]$/) || [])[1] || 0\n      : +(cigar.match(/^(\\d+)([SH])/) || [])[1] || 0\n  }\n}\n","import { BamFile } from '@gmod/bam'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { Region } from '@jbrowse/core/util/types'\nimport {\n  checkAbortSignal,\n  bytesForRegions,\n  updateStatus,\n} from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { toArray } from 'rxjs/operators'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport BamSlightlyLazyFeature from './BamSlightlyLazyFeature'\n\ninterface Header {\n  idToName: string[]\n  nameToId: Record<string, number>\n}\n\nexport default class BamAdapter extends BaseFeatureDataAdapter {\n  private samHeader?: Header\n\n  private setupP?: Promise<Header>\n\n  protected configured?: Promise<{\n    bam: BamFile\n    sequenceAdapter?: BaseFeatureDataAdapter\n  }>\n\n  // derived classes may not use the same configuration so a custom\n  // configure method allows derived classes to override this behavior\n  protected async configure() {\n    if (!this.configured) {\n      const bamLocation = readConfObject(this.config, 'bamLocation')\n      const location = readConfObject(this.config, ['index', 'location'])\n      const indexType = readConfObject(this.config, ['index', 'indexType'])\n      const chunkSizeLimit = readConfObject(this.config, 'chunkSizeLimit')\n      const bam = new BamFile({\n        bamFilehandle: openLocation(bamLocation, this.pluginManager),\n        csiFilehandle:\n          indexType === 'CSI'\n            ? openLocation(location, this.pluginManager)\n            : undefined,\n        baiFilehandle:\n          indexType !== 'CSI'\n            ? openLocation(location, this.pluginManager)\n            : undefined,\n        chunkSizeLimit,\n        fetchSizeLimit: 100_000_000,\n      })\n\n      const adapterConfig = readConfObject(this.config, 'sequenceAdapter')\n      if (adapterConfig && this.getSubAdapter) {\n        this.configured = this.getSubAdapter(adapterConfig).then(\n          ({ dataAdapter }) => ({\n            bam,\n            sequenceAdapter: dataAdapter as BaseFeatureDataAdapter,\n          }),\n        )\n      } else {\n        this.configured = Promise.resolve({ bam })\n      }\n    }\n    return this.configured\n  }\n\n  async getHeader(opts?: BaseOptions) {\n    const { bam } = await this.configure()\n    return bam.getHeaderText(opts)\n  }\n\n  private async setupPre(opts?: BaseOptions) {\n    const { statusCallback = () => {} } = opts || {}\n    const { bam } = await this.configure()\n    this.samHeader = await updateStatus(\n      'Downloading index',\n      statusCallback,\n      async () => {\n        const samHeader = await bam.getHeader(opts)\n\n        // use the @SQ lines in the header to figure out the\n        // mapping between ref ref ID numbers and names\n        const idToName: string[] = []\n        const nameToId: Record<string, number> = {}\n        samHeader\n          .filter(l => l.tag === 'SQ')\n          .forEach((sqLine, refId) => {\n            sqLine.data.forEach(item => {\n              if (item.tag === 'SN') {\n                // this is the ref name\n                const refName = item.value\n                nameToId[refName] = refId\n                idToName[refId] = refName\n              }\n            })\n          })\n\n        return { idToName, nameToId }\n      },\n    )\n    return this.samHeader\n  }\n\n  private async setup(opts?: BaseOptions) {\n    if (!this.setupP) {\n      this.setupP = this.setupPre(opts).catch(e => {\n        this.setupP = undefined\n        throw e\n      })\n    }\n    return this.setupP\n  }\n\n  async getRefNames(opts?: BaseOptions) {\n    const { idToName } = await this.setup(opts)\n    return idToName\n  }\n\n  private async seqFetch(refName: string, start: number, end: number) {\n    const { sequenceAdapter } = await this.configure()\n    const refSeqStore = sequenceAdapter\n    if (!refSeqStore) {\n      return undefined\n    }\n    if (!refName) {\n      return undefined\n    }\n\n    const features = refSeqStore.getFeatures({\n      refName,\n      start,\n      end,\n      assemblyName: '',\n    })\n\n    const seqChunks = await features.pipe(toArray()).toPromise()\n\n    const trimmed: string[] = []\n    seqChunks\n      .sort((a, b) => a.get('start') - b.get('start'))\n      .forEach(chunk => {\n        const chunkStart = chunk.get('start')\n        const chunkEnd = chunk.get('end')\n        const trimStart = Math.max(start - chunkStart, 0)\n        const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart)\n        const trimLength = trimEnd - trimStart\n        const chunkSeq = chunk.get('seq') || chunk.get('residues')\n        trimmed.push(chunkSeq.substr(trimStart, trimLength))\n      })\n\n    const sequence = trimmed.join('')\n    if (sequence.length !== end - start) {\n      throw new Error(\n        `sequence fetch failed: fetching ${refName}:${(\n          start - 1\n        ).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(\n          end - start\n        ).toLocaleString()}`,\n      )\n    }\n    return sequence\n  }\n\n  getFeatures(\n    region: Region & { originalRefName?: string },\n    opts?: BaseOptions,\n  ) {\n    const { refName, start, end, originalRefName } = region\n    const { signal, statusCallback = () => {} } = opts || {}\n    return ObservableCreate<Feature>(async observer => {\n      const { bam } = await this.configure()\n      await this.setup(opts)\n      statusCallback('Downloading alignments')\n      const records = await bam.getRecordsForRange(refName, start, end, opts)\n\n      checkAbortSignal(signal)\n\n      for (const record of records) {\n        let ref: string | undefined\n        if (!record.get('md')) {\n          ref = await this.seqFetch(\n            originalRefName || refName,\n            record.get('start'),\n            record.get('end'),\n          )\n        }\n        observer.next(new BamSlightlyLazyFeature(record, this, ref))\n      }\n      statusCallback('')\n      observer.complete()\n    }, signal)\n  }\n\n  async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {\n    const { bam } = await this.configure()\n    // this is a method to avoid calling on htsget adapters\n    // @ts-ignore\n    if (bam.index.filehandle !== '?') {\n      const bytes = await bytesForRegions(regions, bam)\n      const fetchSizeLimit = readConfObject(this.config, 'fetchSizeLimit')\n      return { bytes, fetchSizeLimit }\n    } else {\n      return super.estimateRegionsStats(regions, opts)\n    }\n  }\n\n  freeResources(/* { region } */): void {}\n\n  // depends on setup being called before the BAM constructor\n  refIdToName(refId: number): string | undefined {\n    return this.samHeader?.idToName[refId]\n  }\n}\n","import { BamFile, HtsgetFile } from '@gmod/bam'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport BamAdapter from '../BamAdapter/BamAdapter'\n\nexport default class HtsgetBamAdapter extends BamAdapter {\n  protected async configure() {\n    if (!this.configured) {\n      const htsgetBase = readConfObject(this.config, 'htsgetBase')\n      const htsgetTrackId = readConfObject(this.config, 'htsgetTrackId')\n      const bam = new HtsgetFile({\n        baseUrl: htsgetBase,\n        trackId: htsgetTrackId,\n      }) as unknown as BamFile\n\n      const adapterConfig = readConfObject(this.config, 'sequenceAdapter')\n      if (adapterConfig && this.getSubAdapter) {\n        this.configured = this.getSubAdapter(adapterConfig).then(\n          ({ dataAdapter }) => {\n            return {\n              bam,\n              sequenceAdapter: dataAdapter as BaseFeatureDataAdapter,\n            }\n          },\n        )\n      }\n      this.configured = Promise.resolve({ bam })\n    }\n    return this.configured\n  }\n}\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  TextField,\n  Typography,\n  makeStyles,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {\n    width: 300,\n  },\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n}))\n\nfunction ColorByTagDlg(props: {\n  model: { setColorScheme: Function }\n  handleClose: () => void\n}) {\n  const classes = useStyles()\n  const { model, handleClose } = props\n  const [tag, setTag] = useState('')\n  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/)\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Color by tag\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent style={{ overflowX: 'hidden' }}>\n        <div className={classes.root}>\n          <Typography>Enter tag to color by: </Typography>\n          <Typography color=\"textSecondary\">\n            Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case)\n            for minimap2 read strand, HP for haplotype, RG for read group, etc.\n          </Typography>\n\n          <TextField\n            value={tag}\n            onChange={event => {\n              setTag(event.target.value)\n            }}\n            placeholder=\"Enter tag name\"\n            inputProps={{\n              maxLength: 2,\n              'data-testid': 'color-tag-name-input',\n            }}\n            error={tag.length === 2 && !validTag}\n            helperText={tag.length === 2 && !validTag ? 'Not a valid tag' : ''}\n            autoComplete=\"off\"\n            data-testid=\"color-tag-name\"\n          />\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            style={{ marginLeft: 20 }}\n            onClick={() => {\n              model.setColorScheme({\n                type: 'tag',\n                tag,\n              })\n              handleClose()\n            }}\n            disabled={!validTag}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n\nexport default observer(ColorByTagDlg)\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  Link,\n  Paper,\n  TextField,\n  Typography,\n  makeStyles,\n} from '@material-ui/core'\n\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {\n    width: 500,\n  },\n  paper: {\n    padding: theme.spacing(2),\n    margin: theme.spacing(2),\n  },\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n  field: {\n    margin: theme.spacing(2),\n  },\n}))\n\nconst flagNames = [\n  'read paired',\n  'read mapped in proper pair',\n  'read unmapped',\n  'mate unmapped',\n  'read reverse strand',\n  'mate reverse strand',\n  'first in pair',\n  'second in pair',\n  'not primary alignment',\n  'read fails platform/vendor quality checks',\n  'read is PCR or optical duplicate',\n  'supplementary alignment',\n]\n\nfunction Bitmask(props: { flag?: number; setFlag: Function }) {\n  const { flag = 0, setFlag } = props\n  return (\n    <>\n      <TextField\n        type=\"number\"\n        value={flag}\n        onChange={event => setFlag(+event.target.value)}\n      />\n      {flagNames.map((name, index) => {\n        const val = flag & (1 << index)\n        const key = `${name}_${val}`\n        return (\n          <div key={key}>\n            <input\n              type=\"checkbox\"\n              checked={Boolean(val)}\n              onChange={event => {\n                if (event.target.checked) {\n                  setFlag(flag | (1 << index))\n                } else {\n                  setFlag(flag & ~(1 << index))\n                }\n              }}\n            />\n            <label htmlFor={key}>{name}</label>\n          </div>\n        )\n      })}\n    </>\n  )\n}\n\nfunction FilterByTagDlg(props: {\n  model: {\n    filterBy?: {\n      flagExclude: number\n      flagInclude: number\n      readName?: string\n      tagFilter?: { tag: string; value: string }\n    }\n    setFilterBy: Function\n  }\n  handleClose: () => void\n}) {\n  const { model, handleClose } = props\n  const classes = useStyles()\n  const { filterBy } = model\n  const [flagInclude, setFlagInclude] = useState(filterBy?.flagInclude)\n  const [flagExclude, setFlagExclude] = useState(filterBy?.flagExclude)\n  const [tag, setTag] = useState(filterBy?.tagFilter?.tag || '')\n  const [tagValue, setTagValue] = useState(filterBy?.tagFilter?.value || '')\n  const [readName, setReadName] = useState(filterBy?.readName || '')\n  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/)\n\n  const site = 'https://broadinstitute.github.io/picard/explain-flags.html'\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Filter options\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <Typography>\n          Set filter bitmask options. Refer to <Link href={site}>{site}</Link>{' '}\n          for details\n        </Typography>\n        <div className={classes.root}>\n          <Paper className={classes.paper} variant=\"outlined\">\n            <div style={{ display: 'flex' }}>\n              <div>\n                <Typography>Read must have ALL these flags</Typography>\n                <Bitmask flag={flagInclude} setFlag={setFlagInclude} />\n              </div>\n              <div>\n                <Typography>Read must have NONE of these flags</Typography>\n                <Bitmask flag={flagExclude} setFlag={setFlagExclude} />\n              </div>\n            </div>\n          </Paper>\n          <Paper className={classes.paper} variant=\"outlined\">\n            <Typography>\n              Filter by tag name and value. Use * in the value field to get all\n              reads containing any value for that tag. Example: filter tag name\n              SA with value * to get all split/supplementary reads. Other\n              examples include HP for haplotype, or RG for read group\n            </Typography>\n            <TextField\n              className={classes.field}\n              value={tag}\n              onChange={event => {\n                setTag(event.target.value)\n              }}\n              placeholder=\"Enter tag name\"\n              inputProps={{\n                maxLength: 2,\n                'data-testid': 'color-tag-name-input',\n              }}\n              error={tag.length === 2 && !validTag}\n              helperText={\n                tag.length === 2 && !validTag ? 'Not a valid tag' : ''\n              }\n              data-testid=\"color-tag-name\"\n            />\n            <TextField\n              className={classes.field}\n              value={tagValue}\n              onChange={event => {\n                setTagValue(event.target.value)\n              }}\n              placeholder=\"Enter tag value\"\n              inputProps={{\n                'data-testid': 'color-tag-name-input',\n              }}\n              data-testid=\"color-tag-value\"\n            />\n          </Paper>\n          <Paper className={classes.paper} variant=\"outlined\">\n            <Typography>Filter by read name</Typography>\n            <TextField\n              className={classes.field}\n              value={readName}\n              onChange={event => {\n                setReadName(event.target.value)\n              }}\n              placeholder=\"Enter read name\"\n              inputProps={{\n                'data-testid': 'color-tag-readname-input',\n              }}\n              data-testid=\"color-tag-readname\"\n            />\n          </Paper>\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            onClick={() => {\n              model.setFilterBy({\n                flagInclude,\n                flagExclude,\n                readName,\n                tagFilter:\n                  tag !== ''\n                    ? {\n                        tag,\n                        value: tagValue,\n                      }\n                    : undefined,\n              })\n              handleClose()\n            }}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n\nexport default observer(FilterByTagDlg)\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  TextField,\n  Typography,\n  makeStyles,\n} from '@material-ui/core'\n\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {\n    margin: 0,\n    padding: theme.spacing(2),\n  },\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n}))\n\nfunction SortByTagDlg(props: {\n  model: { setSortedBy: Function }\n  handleClose: () => void\n}) {\n  const classes = useStyles()\n  const { model, handleClose } = props\n  const [tag, setTag] = useState('')\n  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/)\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Sort by tag\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <div>\n          <Typography>Set the tag to sort by</Typography>\n          <Typography color=\"textSecondary\">\n            Examples: HP for haplotype, RG for read group, etc.\n          </Typography>\n          <TextField\n            value={tag}\n            onChange={event => {\n              setTag(event.target.value)\n            }}\n            placeholder=\"Enter tag name\"\n            inputProps={{\n              maxLength: 2,\n              'data-testid': 'sort-tag-name-input',\n            }}\n            error={tag.length === 2 && !validTag}\n            helperText={tag.length === 2 && !validTag ? 'Not a valid tag' : ''}\n            autoComplete=\"off\"\n            data-testid=\"sort-tag-name\"\n          />\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            onClick={() => {\n              model.setSortedBy('tag', tag)\n              handleClose()\n            }}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\nexport default observer(SortByTagDlg)\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  TextField,\n  Typography,\n  IconButton,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  Checkbox,\n  FormControlLabel,\n  makeStyles,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {\n    margin: theme.spacing(4),\n  },\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n}))\n\nfunction SetFeatureHeightDlg(props: {\n  model: {\n    minScore: number\n    maxScore: number\n    setMinScore: Function\n    setMaxScore: Function\n    setFeatureHeight: Function\n    setNoSpacing: Function\n    featureHeightSetting: number\n    noSpacing: boolean\n  }\n  handleClose: () => void\n}) {\n  const classes = useStyles()\n  const { model, handleClose } = props\n  const { featureHeightSetting, noSpacing: noSpacingSetting } = model\n\n  const [height, setHeight] = useState(`${featureHeightSetting}`)\n  const [noSpacing, setNoSpacing] = useState(noSpacingSetting)\n\n  const ok = height !== '' && !Number.isNaN(+height)\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Set feature height\n        <IconButton className={classes.closeButton} onClick={handleClose}>\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <Typography>\n          Adjust the feature height and whether there is any spacing between\n          features. Setting feature height to 1 and removing spacing makes the\n          display very compact\n        </Typography>\n        <div className={classes.root}>\n          <Typography>Enter feature height: </Typography>\n          <TextField\n            value={height}\n            onChange={event => {\n              setHeight(event.target.value)\n            }}\n          />\n          <FormControlLabel\n            control={\n              <Checkbox\n                checked={!!noSpacing}\n                onChange={() => setNoSpacing(val => !val)}\n              />\n            }\n            label=\"Remove spacing between features in y-direction?\"\n          />\n\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            type=\"submit\"\n            style={{ marginLeft: 20 }}\n            disabled={!ok}\n            onClick={() => {\n              model.setFeatureHeight(\n                height !== '' && !Number.isNaN(+height) ? +height : undefined,\n              )\n              model.setNoSpacing(noSpacing)\n\n              handleClose()\n            }}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n\nexport default observer(SetFeatureHeightDlg)\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  TextField,\n  Typography,\n  makeStyles,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {\n    width: 500,\n  },\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n  field: {\n    margin: theme.spacing(2),\n  },\n}))\n\nfunction SetMaxHeightDlg(props: {\n  model: {\n    maxHeight?: number\n    setMaxHeight: Function\n  }\n  handleClose: () => void\n}) {\n  const { model, handleClose } = props\n  const classes = useStyles()\n  const { maxHeight = '' } = model\n  const [max, setMax] = useState(`${maxHeight}`)\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle id=\"alert-dialog-title\">\n        Filter options\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <div className={classes.root}>\n          <Typography>Set max height for the track</Typography>\n          <TextField\n            value={max}\n            onChange={event => {\n              setMax(event.target.value)\n            }}\n            placeholder=\"Enter max height for layout\"\n          />\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            type=\"submit\"\n            style={{ marginLeft: 20 }}\n            onClick={() => {\n              model.setMaxHeight(\n                max !== '' && !Number.isNaN(+max) ? +max : undefined,\n              )\n              handleClose()\n            }}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n\nexport default observer(SetMaxHeightDlg)\n","import React from 'react'\nimport { observer } from 'mobx-react'\nimport { ObservableMap } from 'mobx'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  Typography,\n  CircularProgress,\n  makeStyles,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {},\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n\n  table: {\n    border: '1px solid #888',\n    margin: theme.spacing(4),\n    '& td': {\n      padding: theme.spacing(1),\n    },\n  },\n}))\n\nfunction ModificationTable({\n  modifications,\n}: {\n  modifications: [string, string][]\n}) {\n  const classes = useStyles()\n  return (\n    <table className={classes.table}>\n      <tbody>\n        {modifications.map(([key, value]) => (\n          <tr key={key}>\n            <td>{key}</td>\n            <td>{value}</td>\n            <td\n              style={{\n                width: '1em',\n                background: value,\n              }}\n            />\n          </tr>\n        ))}\n      </tbody>\n    </table>\n  )\n}\n\nfunction ColorByTagDlg(props: {\n  model: {\n    setColorScheme: Function\n    modificationTagMap: ObservableMap<string, string>\n    colorBy?: { type: string }\n  }\n  handleClose: () => void\n}) {\n  const classes = useStyles()\n  const { model, handleClose } = props\n  const { colorBy, modificationTagMap } = model\n\n  const modifications = [...modificationTagMap.entries()]\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Color by modifications\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <div className={classes.root}>\n          <Typography>\n            You can choose to color the modifications in the BAM/CRAM MM/ML\n            specification using this dialog. Choosing modifications colors the\n            modified positions and can color multiple modification types.\n            Choosing the methylation setting colors methylated and unmethylated\n            CpG.\n          </Typography>\n          <Typography>\n            Note: you can revisit this dialog to see the current mapping of\n            colors to modification type for the modification coloring mode\n          </Typography>\n          <div style={{ margin: 20 }}>\n            {colorBy?.type === 'modifications' ? (\n              <div>\n                {modifications.length ? (\n                  <>\n                    Current modification-type-to-color mapping\n                    <ModificationTable\n                      modifications={[...modificationTagMap.entries()]}\n                    />\n                  </>\n                ) : (\n                  <div>\n                    <Typography>\n                      Note: color by modifications is already enabled. Loading\n                      current modifications...\n                    </Typography>\n                    <CircularProgress size={15} />\n                  </div>\n                )}\n              </div>\n            ) : null}\n            {colorBy?.type === 'methylation' ? (\n              <ModificationTable\n                modifications={[\n                  ['methylated', 'red'],\n                  ['unmethylated', 'blue'],\n                ]}\n              />\n            ) : null}\n          </div>\n          <div style={{ display: 'flex' }}>\n            <Button\n              variant=\"contained\"\n              color=\"primary\"\n              style={{ margin: 5 }}\n              onClick={() => {\n                model.setColorScheme({\n                  type: 'modifications',\n                })\n                handleClose()\n              }}\n            >\n              Modifications\n            </Button>\n            <Button\n              variant=\"contained\"\n              color=\"primary\"\n              style={{ margin: 5 }}\n              onClick={() => {\n                model.setColorScheme({\n                  type: 'methylation',\n                })\n                handleClose()\n              }}\n            >\n              Methylation\n            </Button>\n            <Button\n              variant=\"contained\"\n              color=\"secondary\"\n              style={{ margin: 5 }}\n              onClick={() => handleClose()}\n            >\n              Cancel\n            </Button>\n          </div>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n\nexport default observer(ColorByTagDlg)\n","import React, { useState } from 'react'\nimport {\n  Typography,\n  Link,\n  Paper,\n  Checkbox,\n  FormControlLabel,\n  FormGroup,\n  makeStyles,\n} from '@material-ui/core'\nimport { observer } from 'mobx-react'\nimport { getSession } from '@jbrowse/core/util'\nimport copy from 'copy-to-clipboard'\nimport {\n  FeatureDetails,\n  BaseCard,\n  SimpleValue,\n} from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'\nimport { parseCigar } from '../BamAdapter/MismatchParser'\n\nconst useStyles = makeStyles(() => ({\n  compact: {\n    paddingRight: 0,\n    paddingTop: 0,\n    paddingBottom: 0,\n  },\n}))\n\nconst omit = ['clipPos', 'flags']\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction AlignmentFlags(props: { feature: any }) {\n  const classes = useStyles()\n  const { feature } = props\n  const { flags } = feature\n  const flagNames = [\n    'read paired',\n    'read mapped in proper pair',\n    'read unmapped',\n    'mate unmapped',\n    'read reverse strand',\n    'mate reverse strand',\n    'first in pair',\n    'second in pair',\n    'not primary alignment',\n    'read fails platform/vendor quality checks',\n    'read is PCR or optical duplicate',\n    'supplementary alignment',\n  ]\n  return (\n    <BaseCard {...props} title=\"Flags\">\n      <SimpleValue name={'Flag'} value={flags} />\n\n      <FormGroup>\n        {flagNames.map((name, index) => {\n          const val = flags & (1 << index)\n          const key = `${name}_${val}`\n          return (\n            <FormControlLabel\n              key={key}\n              control={\n                <Checkbox\n                  className={classes.compact}\n                  checked={Boolean(val)}\n                  name={name}\n                  readOnly\n                />\n              }\n              label={name}\n            />\n          )\n        })}\n      </FormGroup>\n    </BaseCard>\n  )\n}\n\nfunction Formatter({ value }: { value: unknown }) {\n  const [show, setShow] = useState(false)\n  const display = String(value)\n  if (display.length > 100) {\n    return (\n      <>\n        <button type=\"button\" onClick={() => copy(display)}>\n          Copy\n        </button>\n        <button type=\"button\" onClick={() => setShow(val => !val)}>\n          {show ? 'Show less' : 'Show more'}\n        </button>\n        <div>{show ? display : `${display.slice(0, 100)}...`}</div>\n      </>\n    )\n  }\n  return <div>{display}</div>\n}\n\n// utility function to get length of alignment from cigar\nfunction getLengthOnRef(cigar: string) {\n  const cigarOps = parseCigar(cigar)\n  let lengthOnRef = 0\n  for (let i = 0; i < cigarOps.length; i += 2) {\n    const len = +cigarOps[i]\n    const op = cigarOps[i + 1]\n    if (op !== 'H' && op !== 'S' && op !== 'I') {\n      lengthOnRef += len\n    }\n  }\n  return lengthOnRef\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction SupplementaryAlignments(props: { tag: string; model: any }) {\n  const { tag, model } = props\n  const session = getSession(model)\n  return (\n    <BaseCard {...props} title=\"Supplementary alignments\">\n      <Typography>List of supplementary alignment locations</Typography>\n      <ul>\n        {tag\n          .split(';')\n          .filter(SA => !!SA)\n          .map((SA, index) => {\n            const [saRef, saStart, saStrand, saCigar] = SA.split(',')\n            const saLength = getLengthOnRef(saCigar)\n            const extra = Math.floor(saLength / 5)\n            const start = +saStart\n            const end = +saStart + saLength\n            const locString = `${saRef}:${Math.max(1, start - extra)}-${\n              end + extra\n            }`\n            const displayStart = start.toLocaleString('en-US')\n            const displayEnd = end.toLocaleString('en-US')\n            const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand})`\n            return (\n              <li key={`${locString}-${index}`}>\n                <Link\n                  onClick={() => {\n                    const { view } = model\n                    try {\n                      if (view) {\n                        view.navToLocString(locString)\n                      } else {\n                        throw new Error(\n                          'No view associated with this view anymore',\n                        )\n                      }\n                    } catch (e) {\n                      console.error(e)\n                      session.notify(`${e}`)\n                    }\n                  }}\n                  href=\"#\"\n                >\n                  {displayString}\n                </Link>\n              </li>\n            )\n          })}\n      </ul>\n    </BaseCard>\n  )\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction PairLink({ locString, model }: { locString: string; model: any }) {\n  const session = getSession(model)\n  return (\n    <Link\n      onClick={() => {\n        const { view } = model\n        try {\n          if (view) {\n            view.navToLocString(locString)\n          } else {\n            session.notify(\n              'No view associated with this feature detail panel anymore',\n              'warning',\n            )\n          }\n        } catch (e) {\n          console.error(e)\n          session.notify(`${e}`)\n        }\n      }}\n      href=\"#\"\n    >\n      {locString}\n    </Link>\n  )\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction AlignmentFeatureDetails(props: { model: any }) {\n  const { model } = props\n  const feat = JSON.parse(JSON.stringify(model.featureData))\n  const SA = (feat.tags && feat.tags.SA) || feat.SA\n  return (\n    <Paper data-testid=\"alignment-side-drawer\">\n      <FeatureDetails\n        {...props}\n        omit={omit}\n        feature={feat}\n        formatter={(value: unknown, key: string) => {\n          return key === 'next_segment_position' ? (\n            <PairLink model={model} locString={value as string} />\n          ) : (\n            <Formatter value={value} />\n          )\n        }}\n      />\n      {SA ? <SupplementaryAlignments model={model} tag={SA} /> : null}\n      <AlignmentFlags feature={feat} {...props} />\n    </Paper>\n  )\n}\n\nexport default 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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 { revcom } from '@jbrowse/core/util'\nexport interface Mismatch {\n  qual?: number\n  start: number\n  length: number\n  type: string\n  base: string\n  altbase?: string\n  seq?: string\n  cliplen?: number\n}\n\nexport function parseCigar(cigar: string) {\n  return (cigar || '').split(/([MIDNSHPX=])/)\n}\nexport function cigarToMismatches(\n  ops: string[],\n  seq: string,\n  qual?: Buffer,\n): Mismatch[] {\n  let currOffset = 0\n  let seqOffset = 0\n  const mismatches: Mismatch[] = []\n  for (let i = 0; i < ops.length - 1; i += 2) {\n    const len = +ops[i]\n    const op = ops[i + 1]\n    if (op === 'M' || op === '=' || op === 'E') {\n      seqOffset += len\n    }\n    if (op === 'I') {\n      mismatches.push({\n        start: currOffset,\n        type: 'insertion',\n        base: `${len}`,\n        length: 0,\n      })\n      seqOffset += len\n    } else if (op === 'D') {\n      mismatches.push({\n        start: currOffset,\n        type: 'deletion',\n        base: '*',\n        length: len,\n      })\n    } else if (op === 'N') {\n      mismatches.push({\n        start: currOffset,\n        type: 'skip',\n        base: 'N',\n        length: len,\n      })\n    } else if (op === 'X') {\n      const r = seq.slice(seqOffset, seqOffset + len)\n      const q = qual?.slice(seqOffset, seqOffset + len) || []\n\n      for (let j = 0; j < len; j++) {\n        mismatches.push({\n          start: currOffset + j,\n          type: 'mismatch',\n          base: r[j],\n          qual: q[j],\n          length: 1,\n        })\n      }\n      seqOffset += len\n    } else if (op === 'H') {\n      mismatches.push({\n        start: currOffset,\n        type: 'hardclip',\n        base: `H${len}`,\n        cliplen: len,\n        length: 1,\n      })\n    } else if (op === 'S') {\n      mismatches.push({\n        start: currOffset,\n        type: 'softclip',\n        base: `S${len}`,\n        cliplen: len,\n        length: 1,\n      })\n      seqOffset += len\n    }\n\n    if (op !== 'I' && op !== 'S' && op !== 'H') {\n      currOffset += len\n    }\n  }\n  return mismatches\n}\n\n/**\n * parse a SAM MD tag to find mismatching bases of the template versus the reference\n * @returns array of mismatches and their positions\n */\nexport function mdToMismatches(\n  mdstring: string,\n  cigarOps: string[],\n  cigarMismatches: Mismatch[],\n  seq: string,\n  qual?: Buffer,\n): Mismatch[] {\n  const mismatchRecords: Mismatch[] = []\n  let curr: Mismatch = { start: 0, base: '', length: 0, type: 'mismatch' }\n  const skips = cigarMismatches.filter(cigar => cigar.type === 'skip')\n  let lastCigar = 0\n  let lastTemplateOffset = 0\n  let lastRefOffset = 0\n  let lastSkipPos = 0\n\n  // convert a position on the reference sequence to a position\n  // on the template sequence, taking into account hard and soft\n  // clipping of reads\n\n  function nextRecord(): void {\n    mismatchRecords.push(curr)\n\n    // get a new mismatch record ready\n    curr = {\n      start: curr.start + curr.length,\n      length: 0,\n      base: '',\n      type: 'mismatch',\n    }\n  }\n\n  function getTemplateCoordLocal(refCoord: number): number {\n    let templateOffset = lastTemplateOffset\n    let refOffset = lastRefOffset\n    for (\n      let i = lastCigar;\n      i < cigarOps.length && refOffset <= refCoord;\n      i += 2, lastCigar = i\n    ) {\n      const len = +cigarOps[i]\n      const op = cigarOps[i + 1]\n      if (op === 'S' || op === 'I') {\n        templateOffset += len\n      } else if (op === 'D' || op === 'P' || op === 'N') {\n        refOffset += len\n      } else if (op !== 'H') {\n        templateOffset += len\n        refOffset += len\n      }\n    }\n    lastTemplateOffset = templateOffset\n    lastRefOffset = refOffset\n\n    return templateOffset - (refOffset - refCoord)\n  }\n\n  // now actually parse the MD string\n  const md = mdstring.match(/(\\d+|\\^[a-z]+|[a-z])/gi) || []\n  for (let i = 0; i < md.length; i++) {\n    const token = md[i]\n    const num = +token\n    if (!Number.isNaN(num)) {\n      curr.start += num\n    } else if (token.startsWith('^')) {\n      curr.length = token.length - 1\n      curr.base = '*'\n      curr.type = 'deletion'\n      curr.seq = token.substring(1)\n      nextRecord()\n    } else {\n      // mismatch\n      for (let j = 0; j < token.length; j += 1) {\n        curr.length = 1\n\n        while (lastSkipPos < skips.length) {\n          const mismatch = skips[lastSkipPos]\n          if (curr.start >= mismatch.start) {\n            curr.start += mismatch.length\n            lastSkipPos++\n          } else {\n            break\n          }\n        }\n        const s = cigarOps ? getTemplateCoordLocal(curr.start) : curr.start\n        curr.base = seq ? seq.substr(s, 1) : 'X'\n        const qualScore = qual?.slice(s, s + 1)[0]\n        if (qualScore) {\n          curr.qual = qualScore\n        }\n        curr.altbase = token\n        nextRecord()\n      }\n    }\n  }\n  return mismatchRecords\n}\n\nexport function getTemplateCoord(refCoord: number, cigarOps: string[]): number {\n  let templateOffset = 0\n  let refOffset = 0\n  for (let i = 0; i < cigarOps.length && refOffset <= refCoord; i += 2) {\n    const len = +cigarOps[i]\n    const op = cigarOps[i + 1]\n    if (op === 'S' || op === 'I') {\n      templateOffset += len\n    } else if (op === 'D' || op === 'P') {\n      refOffset += len\n    } else if (op !== 'H') {\n      templateOffset += len\n      refOffset += len\n    }\n  }\n  return templateOffset - (refOffset - refCoord)\n}\n\nexport function getMismatches(\n  cigarString: string,\n  mdString: string,\n  seq: string,\n  qual?: Buffer,\n): Mismatch[] {\n  let mismatches: Mismatch[] = []\n  let cigarOps: string[] = []\n\n  // parse the CIGAR tag if it has one\n  if (cigarString) {\n    cigarOps = parseCigar(cigarString)\n    mismatches = mismatches.concat(cigarToMismatches(cigarOps, seq, qual))\n  }\n\n  // now let's look for CRAM or MD mismatches\n  if (mdString) {\n    mismatches = mismatches.concat(\n      mdToMismatches(mdString, cigarOps, mismatches, seq, qual),\n    )\n  }\n\n  // uniqify the mismatches\n  const seen: { [index: string]: boolean } = {}\n  return mismatches.filter(m => {\n    const key = `${m.type},${m.start},${m.length}`\n    const s = seen[key]\n    seen[key] = true\n    return !s\n  })\n}\n\n// adapted from minimap2 code static void write_MD_core function\nexport function generateMD(target: string, query: string, cigar: string) {\n  let queryOffset = 0\n  let targetOffset = 0\n  let lengthMD = 0\n  if (!target) {\n    console.warn('no ref supplied to generateMD')\n    return ''\n  }\n  const cigarOps = parseCigar(cigar)\n  let str = ''\n  for (let i = 0; i < cigarOps.length; i += 2) {\n    const len = +cigarOps[i]\n    const op = cigarOps[i + 1]\n    if (op === 'M' || op === 'X' || op === '=') {\n      for (let j = 0; j < len; j++) {\n        if (\n          query[queryOffset + j].toLowerCase() !==\n          target[targetOffset + j].toLowerCase()\n        ) {\n          str += `${lengthMD}${target[targetOffset + j].toUpperCase()}`\n          lengthMD = 0\n        } else {\n          lengthMD++\n        }\n      }\n      queryOffset += len\n      targetOffset += len\n    } else if (op === 'I') {\n      queryOffset += len\n    } else if (op === 'D') {\n      let tmp = ''\n      for (let j = 0; j < len; j++) {\n        tmp += target[targetOffset + j].toUpperCase()\n      }\n      str += `${lengthMD}^${tmp}`\n      lengthMD = 0\n      targetOffset += len\n    } else if (op === 'N') {\n      targetOffset += len\n    } else if (op === 'S') {\n      queryOffset += len\n    }\n  }\n  if (lengthMD > 0) {\n    str += lengthMD\n  }\n  return str\n}\n\n// get relative reference sequence positions for positions given relative to\n// the read sequence\nexport function* getNextRefPos(cigarOps: string[], positions: number[]) {\n  let cigarIdx = 0\n  let readPos = 0\n  let refPos = 0\n\n  for (let i = 0; i < positions.length; i++) {\n    const pos = positions[i]\n    for (; cigarIdx < cigarOps.length && readPos < pos; cigarIdx += 2) {\n      const len = +cigarOps[cigarIdx]\n      const op = cigarOps[cigarIdx + 1]\n      if (op === 'S' || op === 'I') {\n        readPos += len\n      } else if (op === 'D' || op === 'N') {\n        refPos += len\n      } else if (op === 'M' || op === 'X' || op === '=') {\n        readPos += len\n        refPos += len\n      }\n    }\n\n    yield positions[i] - readPos + refPos\n  }\n}\n\nexport function getModificationPositions(\n  mm: string,\n  fseq: string,\n  fstrand: number,\n) {\n  const seq = fstrand === -1 ? revcom(fseq) : fseq\n  return mm\n    .split(';')\n    .filter(mod => !!mod)\n    .map(mod => {\n      const [basemod, ...skips] = mod.split(',')\n\n      // regexes based on parse_mm.pl from hts-specs\n      const matches = basemod.match(/([A-Z])([-+])([^,.?]+)([.?])?/)\n      if (!matches) {\n        throw new Error('bad format for MM tag')\n      }\n      const [, base, strand, typestr] = matches\n\n      // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so\n      // split, and they can also be chemical codes (ChEBI) e.g. C+16061\n      const types = typestr.split(/(\\d+|.)/).filter(f => !!f)\n\n      if (strand === '-') {\n        console.warn('unsupported negative strand modifications')\n        // make sure to return a somewhat matching type even in this case\n        return { type: 'unsupported', positions: [] }\n      }\n\n      // this logic also based on parse_mm.pl from hts-specs is that in the\n      // sequence of the read, if we have a modification type e.g. C+m;2 and a\n      // sequence ACGTACGTAC we skip the two instances of C and go to the last\n      // C\n      return types.map(type => {\n        let i = 0\n        return {\n          type,\n          positions: skips\n            .map(score => +score)\n            .map(delta => {\n              do {\n                if (base === 'N' || base === seq[i]) {\n                  delta--\n                }\n                i++\n              } while (delta >= 0 && i < seq.length)\n              const temp = i - 1\n              return fstrand === -1 ? seq.length - 1 - temp : temp\n            })\n            .sort((a, b) => a - b),\n        }\n      })\n    })\n    .flat()\n}\n\nexport function getModificationTypes(mm: string) {\n  const mods = mm.split(';')\n  return mods\n    .filter(mod => !!mod)\n    .map(mod => {\n      const [basemod] = mod.split(',')\n\n      const matches = basemod.match(/([A-Z])([-+])([^,]+)/)\n      if (!matches) {\n        throw new Error('bad format for MM tag')\n      }\n      const [, , , typestr] = matches\n\n      // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so\n      // split, and they can also be chemical codes (ChEBI) e.g. C+16061\n      return typestr.split(/(\\d+|.)/).filter(f => !!f)\n    })\n    .flat()\n}\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default (pluginManager: PluginManager) => {\n  return types.late(() =>\n    ConfigurationSchema(\n      'CramAdapter',\n      {\n        fetchSizeLimit: {\n          type: 'number',\n          defaultValue: 3_000_000,\n        },\n        cramLocation: {\n          type: 'fileLocation',\n          defaultValue: {\n            uri: '/path/to/my.cram',\n            locationType: 'UriLocation',\n          },\n        },\n        craiLocation: {\n          type: 'fileLocation',\n          defaultValue: {\n            uri: '/path/to/my.cram.crai',\n            locationType: 'UriLocation',\n          },\n        },\n        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),\n      },\n      { explicitlyTyped: true },\n    ),\n  )\n}\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\n\n// locals\nimport configSchemaF from './configSchema'\n\nexport default (pluginManager: PluginManager) => {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'CramAdapter',\n        configSchema: pluginManager.load(configSchemaF),\n        getAdapterClass: () => import('./CramAdapter').then(r => r.default),\n      }),\n  )\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default types.late(() =>\n  ConfigurationSchema(\n    'BamAdapter',\n    {\n      bamLocation: {\n        type: 'fileLocation',\n        defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },\n      },\n      index: ConfigurationSchema('BamIndex', {\n        indexType: {\n          model: types.enumeration('IndexType', ['BAI', 'CSI']),\n          type: 'stringEnum',\n          defaultValue: 'BAI',\n        },\n        location: {\n          type: 'fileLocation',\n          defaultValue: {\n            uri: '/path/to/my.bam.bai',\n            locationType: 'UriLocation',\n          },\n        },\n      }),\n      chunkSizeLimit: {\n        type: 'number',\n        defaultValue: 100_000_000,\n      },\n      fetchSizeLimit: {\n        type: 'number',\n        defaultValue: 5_000_000,\n      },\n      sequenceAdapter: {\n        type: 'frozen',\n        defaultValue: null,\n      },\n    },\n    { explicitlyTyped: true },\n  ),\n)\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport configSchema from './configSchema'\n\nexport default (pluginManager: PluginManager) => {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'BamAdapter',\n        configSchema,\n        getAdapterClass: () => import('./BamAdapter').then(r => r.default),\n      }),\n  )\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default types.late(() =>\n  ConfigurationSchema(\n    'HtsgetBamAdapter',\n    {\n      htsgetBase: {\n        type: 'string',\n        defaultValue: '',\n      },\n      htsgetTrackId: {\n        type: 'string',\n        defaultValue: '',\n      },\n      sequenceAdapter: {\n        type: 'frozen',\n        defaultValue: null,\n      },\n    },\n    { explicitlyTyped: true },\n  ),\n)\n","import configSchema from './configSchema'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\n\nexport default (pluginManager: PluginManager) => {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'HtsgetBamAdapter',\n        adapterMetadata: {\n          category: null,\n          hiddenFromGUI: true,\n          displayName: null,\n          description: null,\n        },\n        configSchema,\n        getAdapterClass: () =>\n          import('./HtsgetBamAdapter').then(r => r.default),\n      }),\n  )\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { types } from 'mobx-state-tree'\n\nexport default (pluginManager: PluginManager) =>\n  types.late(() =>\n    ConfigurationSchema(\n      'SNPCoverageAdapter',\n      {\n        subadapter: pluginManager.pluggableConfigSchemaType('adapter'),\n      },\n      { explicitlyTyped: true },\n    ),\n  )\n","import { Feature } from '@jbrowse/core/util/simpleFeature'\n// get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and\n// BAM does not\nexport function getTag(feature: Feature, tag: string) {\n  const tags = feature.get('tags')\n  return tags ? tags[tag] : feature.get(tag)\n}\n\n// use fallback alt tag, used in situations where upper case/lower case tags\n// exist e.g. Mm/MM for base modifications\nexport function getTagAlt(feature: Feature, tag: string, alt: string) {\n  return getTag(feature, tag) || getTag(feature, alt)\n}\n\n// orientation definitions from igv.js, see also\n// https://software.broadinstitute.org/software/igv/interpreting_pair_orientations\nexport const orientationTypes = {\n  fr: {\n    F1R2: 'LR',\n    F2R1: 'LR',\n\n    F1F2: 'LL',\n    F2F1: 'LL',\n\n    R1R2: 'RR',\n    R2R1: 'RR',\n\n    R1F2: 'RL',\n    R2F1: 'RL',\n  } as { [key: string]: string },\n\n  rf: {\n    R1F2: 'LR',\n    R2F1: 'LR',\n\n    R1R2: 'LL',\n    R2R1: 'LL',\n\n    F1F2: 'RR',\n    F2F1: 'RR',\n\n    F1R2: 'RL',\n    F2R1: 'RL',\n  } as { [key: string]: string },\n\n  ff: {\n    F2F1: 'LR',\n    R1R2: 'LR',\n\n    F2R1: 'LL',\n    R1F2: 'LL',\n\n    R2F1: 'RR',\n    F1R2: 'RR',\n\n    R2R1: 'RL',\n    F1F2: 'RL',\n  } as { [key: string]: string },\n}\n\nexport function getColorWGBS(strand: number, base: string) {\n  if (strand === 1) {\n    if (base === 'C') {\n      return '#f00'\n    }\n    if (base === 'T') {\n      return '#00f'\n    }\n  } else if (strand === -1) {\n    if (base === 'G') {\n      return '#f00'\n    }\n    if (base === 'A') {\n      return '#00f'\n    }\n  }\n  return '#888'\n}\n","import {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { AugmentedRegion as Region } from '@jbrowse/core/util/types'\nimport SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { reduce, filter, toArray } from 'rxjs/operators'\nimport { Observable } from 'rxjs'\nimport { getTag, getTagAlt } from '../util'\nimport {\n  parseCigar,\n  getNextRefPos,\n  getModificationPositions,\n  Mismatch,\n} from '../BamAdapter/MismatchParser'\n\ninterface SNPCoverageOptions extends BaseOptions {\n  filters?: SerializableFilterChain\n}\n\nfunction mismatchLen(mismatch: Mismatch) {\n  return !isInterbase(mismatch.type) ? mismatch.length : 1\n}\n\nfunction isInterbase(type: string) {\n  return type === 'softclip' || type === 'hardclip' || type === 'insertion'\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction inc(bin: any, strand: number, type: string, field: string) {\n  if (!bin[type][field]) {\n    bin[type][field] = { total: 0, strands: { '-1': 0, '0': 0, '1': 0 } }\n  }\n  bin[type][field].total++\n  bin[type][field].strands[strand]++\n}\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction dec(bin: any, strand: number, type: string, field: string) {\n  if (!bin[type][field]) {\n    bin[type][field] = { total: 0, strands: { '-1': 0, '0': 0, '1': 0 } }\n  }\n  bin[type][field].total--\n  bin[type][field].strands[strand]--\n}\n\nexport default class SNPCoverageAdapter extends BaseFeatureDataAdapter {\n  protected async configure() {\n    const subadapterConfig = readConfObject(this.config, 'subadapter')\n    const sequenceConf = readConfObject(this.config, [\n      'subadapter',\n      'sequenceAdapter',\n    ])\n    const dataAdapter = await this.getSubAdapter?.(subadapterConfig)\n\n    const sequenceAdapter = sequenceConf\n      ? await this.getSubAdapter?.(sequenceConf)\n      : undefined\n\n    if (!dataAdapter) {\n      throw new Error('Failed to get subadapter')\n    }\n\n    return {\n      subadapter: dataAdapter.dataAdapter as BaseFeatureDataAdapter,\n      sequenceAdapter: sequenceAdapter?.dataAdapter as\n        | BaseFeatureDataAdapter\n        | undefined,\n    }\n  }\n\n  getFeatures(region: Region, opts: SNPCoverageOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const { subadapter } = await this.configure()\n      let stream = subadapter.getFeatures(region, opts)\n\n      if (opts.filters) {\n        const { filters } = opts\n        stream = stream.pipe(filter(f => filters.passes(f, opts)))\n      }\n\n      const { bins, skipmap } = await this.generateCoverageBins(\n        stream,\n        region,\n        opts,\n      )\n\n      bins.forEach((bin, index) => {\n        observer.next(\n          new SimpleFeature({\n            id: `${this.id}-${region.start}-${index}`,\n            data: {\n              score: bin.total,\n              snpinfo: bin,\n              start: region.start + index,\n              end: region.start + index + 1,\n              refName: region.refName,\n            },\n          }),\n        )\n      })\n\n      // make fake features from the coverage\n      Object.entries(skipmap).forEach(([key, skip]) => {\n        observer.next(\n          new SimpleFeature({\n            id: key,\n            data: {\n              type: 'skip',\n              start: skip.start,\n              end: skip.end,\n              strand: skip.strand,\n              score: skip.score,\n              xs: skip.xs,\n            },\n          }),\n        )\n      })\n\n      observer.complete()\n    }, opts.signal)\n  }\n\n  async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {\n    const { subadapter } = await this.configure()\n    return subadapter.estimateRegionsStats(regions, opts)\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    const { subadapter } = await this.configure()\n    return subadapter.getRefNames(opts)\n  }\n\n  freeResources(/* { region } */): void {}\n\n  /**\n   * Generates coverage bins from features which details\n   * the reference, mismatches, strands, and coverage info\n   * @param features - Features of region to be passed in\n   * @param region - Region\n   * @param bpPerPx - base pairs per pixel\n   * @returns Array of nested frequency tables\n   */\n  async generateCoverageBins(\n    features: Observable<Feature>,\n    region: Region,\n    opts: { bpPerPx?: number; colorBy?: { type: string; tag?: string } },\n  ) {\n    const { colorBy } = opts\n    const { sequenceAdapter } = await this.configure()\n    const { originalRefName, refName, start, end } = region\n    const binMax = Math.ceil(region.end - region.start)\n\n    const skipmap = {} as {\n      [key: string]: {\n        score: number\n        feature: unknown\n        start: number\n        end: number\n        strand: number\n        xs: string\n      }\n    }\n\n    // bins contain cov feature if they contribute to coverage, or noncov which\n    // are interbase or other features that don't contribute to coverage.\n    // delskips are elements that don't contribute to coverage, but should be\n    // reported also (and are not interbase)\n    type BinType = { total: number; strands: { [key: string]: number } }\n\n    // request an extra +1 on the end to get CpG crossing region boundary\n    let regionSeq: string | undefined\n\n    if (sequenceAdapter) {\n      const [feat] = await sequenceAdapter\n        .getFeatures({\n          refName: originalRefName || refName,\n          start,\n          end: end + 1,\n          assemblyName: region.assemblyName,\n        })\n        .pipe(toArray())\n        .toPromise()\n      regionSeq = feat?.get('seq')\n    }\n\n    const bins = await features\n      .pipe(\n        reduce(\n          (bins, feature) => {\n            const cigar = feature.get('CIGAR')\n            const fstart = feature.get('start')\n            const fend = feature.get('end')\n            const fstrand = feature.get('strand')\n            const cigarOps = parseCigar(cigar)\n\n            for (let j = fstart; j < fend + 1; j++) {\n              const i = j - region.start\n              if (i >= 0 && i < binMax) {\n                const bin = bins[i] || {\n                  total: 0,\n                  lowqual: {} as BinType,\n                  cov: {} as BinType,\n                  delskips: {} as BinType,\n                  noncov: {} as BinType,\n                  ref: {} as BinType,\n                }\n                if (j !== fend) {\n                  bin.total++\n                  inc(bin, fstrand, 'ref', 'ref')\n                }\n                bins[i] = bin\n              }\n            }\n\n            if (colorBy?.type === 'modifications') {\n              const seq = feature.get('seq')\n              const mm = getTagAlt(feature, 'MM', 'Mm') || ''\n\n              const ml =\n                (getTagAlt(feature, 'ML', 'Ml') as number[] | string) || []\n\n              const probabilities = ml\n                ? (typeof ml === 'string'\n                    ? ml.split(',').map(e => +e)\n                    : ml\n                  ).map(e => e / 255)\n                : (getTagAlt(feature, 'MP', 'Mp') as string)\n                    .split('')\n                    .map(s => s.charCodeAt(0) - 33)\n                    .map(elt => Math.min(1, elt / 50))\n\n              let probIndex = 0\n              getModificationPositions(mm, seq, fstrand).forEach(\n                ({ type, positions }) => {\n                  const mod = `mod_${type}`\n                  for (const pos of getNextRefPos(cigarOps, positions)) {\n                    const epos = pos + fstart - region.start\n                    if (\n                      epos >= 0 &&\n                      epos < bins.length &&\n                      pos + fstart < fend\n                    ) {\n                      const bin = bins[epos] || {\n                        total: 0,\n                        lowqual: {} as BinType,\n                        cov: {} as BinType,\n                        delskips: {} as BinType,\n                        noncov: {} as BinType,\n                        ref: {} as BinType,\n                      }\n\n                      if (probabilities[probIndex] > 0.5) {\n                        inc(bin, fstrand, 'cov', mod)\n                      } else {\n                        inc(bin, fstrand, 'lowqual', mod)\n                      }\n                    }\n                    probIndex++\n                  }\n                },\n              )\n            }\n\n            // methylation based coloring takes into account both reference\n            // sequence CpG detection and reads\n            else if (colorBy?.type === 'methylation') {\n              if (!regionSeq) {\n                throw new Error(\n                  'no region sequence detected, need sequenceAdapter configuration',\n                )\n              }\n              const seq = feature.get('seq')\n              const mm = getTagAlt(feature, 'MM', 'Mm') || ''\n              const methBins = new Array(region.end - region.start).fill(0)\n\n              getModificationPositions(mm, seq, fstrand).forEach(\n                ({ type, positions }) => {\n                  // we are processing methylation\n                  if (type === 'm') {\n                    for (const pos of getNextRefPos(cigarOps, positions)) {\n                      const epos = pos + fstart - region.start\n                      if (epos >= 0 && epos < methBins.length) {\n                        methBins[epos] = 1\n                      }\n                    }\n                  }\n                },\n              )\n\n              for (let j = fstart; j < fend; j++) {\n                const i = j - region.start\n                if (i >= 0 && i < bins.length - 1) {\n                  const l1 = regionSeq[i].toLowerCase()\n                  const l2 = regionSeq[i + 1].toLowerCase()\n                  const bin = bins[i]\n                  const bin1 = bins[i + 1]\n\n                  // color\n                  if (l1 === 'c' && l2 === 'g') {\n                    if (methBins[i] || methBins[i + 1]) {\n                      inc(bin, fstrand, 'cov', 'meth')\n                      inc(bin1, fstrand, 'cov', 'meth')\n                      dec(bin, fstrand, 'ref', 'ref')\n                      dec(bin1, fstrand, 'ref', 'ref')\n                    } else {\n                      inc(bin, fstrand, 'cov', 'unmeth')\n                      inc(bin1, fstrand, 'cov', 'unmeth')\n                      dec(bin, fstrand, 'ref', 'ref')\n                      dec(bin1, fstrand, 'ref', 'ref')\n                    }\n                  }\n                }\n              }\n            }\n\n            // normal SNP based coloring\n            else {\n              const mismatches = feature.get('mismatches') as\n                | Mismatch[]\n                | undefined\n\n              if (mismatches) {\n                for (let i = 0; i < mismatches.length; i++) {\n                  const mismatch = mismatches[i]\n                  const ms = fstart + mismatch.start\n                  for (let j = ms; j < ms + mismatchLen(mismatch); j++) {\n                    const epos = j - region.start\n                    if (epos >= 0 && epos < bins.length) {\n                      const bin = bins[epos]\n                      const { base, type } = mismatch\n                      const interbase = isInterbase(type)\n                      if (!interbase) {\n                        dec(bin, fstrand, 'ref', 'ref')\n                      } else {\n                        inc(bin, fstrand, 'noncov', type)\n                      }\n\n                      if (type === 'deletion' || type === 'skip') {\n                        inc(bin, fstrand, 'delskips', type)\n                        bin.total--\n                      } else if (!interbase) {\n                        inc(bin, fstrand, 'cov', base)\n                      }\n                    }\n                  }\n                }\n\n                mismatches\n                  .filter(mismatch => mismatch.type === 'skip')\n                  .forEach(mismatch => {\n                    const mstart = feature.get('start') + mismatch.start\n                    const start = mstart\n                    const end = mstart + mismatch.length\n                    const strand = feature.get('strand')\n                    const hash = `${start}_${end}_${strand}`\n                    if (!skipmap[hash]) {\n                      skipmap[hash] = {\n                        feature: feature,\n                        start,\n                        end,\n                        strand,\n                        xs: getTag(feature, 'XS') || getTag(feature, 'TS'),\n                        score: 1,\n                      }\n                    } else {\n                      skipmap[hash].score++\n                    }\n                  })\n              }\n            }\n\n            return bins\n          },\n          [] as {\n            total: number\n            lowqual: BinType\n            cov: BinType\n            delskips: BinType\n            noncov: BinType\n            ref: BinType\n          }[],\n        ),\n      )\n      .toPromise()\n\n    return { bins, skipmap }\n  }\n}\n\nconst { capabilities } = SNPCoverageAdapter\nexport { capabilities }\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'\nimport configSchemaFactory from './configSchema'\nimport { capabilities } from './SNPCoverageAdapter'\n\nexport default (pluginManager: PluginManager) => {\n  pluginManager.addAdapterType(\n    () =>\n      new AdapterType({\n        name: 'SNPCoverageAdapter',\n        adapterMetadata: {\n          category: null,\n          displayName: null,\n          hiddenFromGUI: true,\n          description: null,\n        },\n        getAdapterClass: () =>\n          import('./SNPCoverageAdapter').then(r => r.default),\n        configSchema: configSchemaFactory(pluginManager),\n        adapterCapabilities: capabilities,\n      }),\n  )\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nexport default ConfigurationSchema(\n  'SNPCoverageRenderer',\n  {\n    clipColor: {\n      type: 'color',\n      description: 'the color of the clipping marker',\n      defaultValue: 'red',\n    },\n    indicatorThreshold: {\n      type: 'number',\n      description:\n        'the proportion of reads containing a insertion/clip indicator',\n      defaultValue: 0.4,\n    },\n    drawArcs: {\n      type: 'boolean',\n      description: 'Draw sashimi-style arcs for intron features',\n      defaultValue: true,\n    },\n    drawInterbaseCounts: {\n      type: 'boolean',\n      description:\n        'draw count \"upsidedown histogram\" of the interbase events that don\\'t contribute to the coverage count so are not drawn in the normal histogram',\n      defaultValue: true,\n    },\n    drawIndicators: {\n      type: 'boolean',\n      description:\n        'draw a triangular indicator where an event has been detected',\n      defaultValue: true,\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import { createJBrowseTheme } from '@jbrowse/core/ui'\nimport { featureSpanPx, bpSpanPx } from '@jbrowse/core/util'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'\nimport {\n  getOrigin,\n  getScale,\n  ScaleOpts,\n  WiggleBaseRenderer,\n  YSCALEBAR_LABEL_OFFSET,\n} from '@jbrowse/plugin-wiggle'\n\nexport interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {\n  bpPerPx: number\n  height: number\n  highResolutionScaling: number\n  scaleOpts: ScaleOpts\n}\n\nexport interface RenderArgsDeserializedWithFeatures\n  extends RenderArgsDeserialized {\n  features: Map<string, Feature>\n  ticks: { values: number[] }\n  displayCrossHatches: boolean\n  modificationTagMap?: Record<string, string>\n}\n\ntype Counts = {\n  [key: string]: { total: number; strands: { [key: string]: number } }\n}\n\ninterface SNPInfo {\n  cov: Counts\n  noncov: Counts\n  total: number\n}\n\nexport default class SNPCoverageRenderer extends WiggleBaseRenderer {\n  // note: the snps are drawn on linear scale even if the data is drawn in log\n  // scape hence the two different scales being used\n  draw(\n    ctx: CanvasRenderingContext2D,\n    props: RenderArgsDeserializedWithFeatures,\n  ) {\n    const {\n      features,\n      regions,\n      bpPerPx,\n      displayCrossHatches,\n      modificationTagMap = {},\n      scaleOpts,\n      height: unadjustedHeight,\n      theme: configTheme,\n      config: cfg,\n      ticks,\n    } = props\n    const theme = createJBrowseTheme(configTheme)\n    const [region] = regions\n    const width = (region.end - region.start) / bpPerPx\n\n    // the adjusted height takes into account YSCALEBAR_LABEL_OFFSET from the\n    // wiggle display, and makes the height of the actual drawn area add\n    // \"padding\" to the top and bottom of the display\n    const offset = YSCALEBAR_LABEL_OFFSET\n    const height = unadjustedHeight - offset * 2\n\n    const { domain } = scaleOpts\n    if (!domain) {\n      return\n    }\n    const opts = { ...scaleOpts, range: [0, height] }\n    const viewScale = getScale(opts)\n    const snpViewScale = getScale({\n      ...opts,\n      range: [0, height],\n      scaleType: 'linear',\n    })\n    // clipping and insertion indicators, uses a smaller height/2 scale\n    const indicatorViewScale = getScale({\n      ...opts,\n      range: [0, height / 2],\n      scaleType: 'linear',\n    })\n    const originY = getOrigin(scaleOpts.scaleType)\n    const snpOriginY = getOrigin('linear')\n\n    const indicatorThreshold = readConfObject(cfg, 'indicatorThreshold')\n    const drawInterbaseCounts = readConfObject(cfg, 'drawInterbaseCounts')\n    const drawArcs = readConfObject(cfg, 'drawArcs')\n    const drawIndicators = readConfObject(cfg, 'drawIndicators')\n\n    // get the y coordinate that we are plotting at, this can be log scale\n    const toY = (n: number) => height - (viewScale(n) || 0) + offset\n    const toHeight = (n: number) => toY(originY) - toY(n)\n\n    // this is always linear scale, even when plotted on top of log scale\n    const snpToY = (n: number) => height - (snpViewScale(n) || 0) + offset\n    const indicatorToY = (n: number) =>\n      height - (indicatorViewScale(n) || 0) + offset\n    const snpToHeight = (n: number) => snpToY(snpOriginY) - snpToY(n)\n    const indicatorToHeight = (n: number) =>\n      indicatorToY(snpOriginY) - indicatorToY(n)\n\n    const colorForBase: { [key: string]: string } = {\n      A: theme.palette.bases.A.main,\n      C: theme.palette.bases.C.main,\n      G: theme.palette.bases.G.main,\n      T: theme.palette.bases.T.main,\n      total: 'lightgrey',\n      insertion: 'purple',\n      softclip: 'blue',\n      hardclip: 'red',\n      meth: 'red',\n      unmeth: 'blue',\n      ref: 'lightgrey',\n    }\n\n    const feats = [...features.values()]\n    const coverage = feats.filter(f => f.get('type') !== 'skip')\n    const skips = feats.filter(f => f.get('type') === 'skip')\n\n    // Use two pass rendering, which helps in visualizing the SNPs at higher\n    // bpPerPx First pass: draw the gray background\n    ctx.fillStyle = colorForBase.total\n    for (let i = 0; i < coverage.length; i++) {\n      const feature = coverage[i]\n      const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)\n      const w = rightPx - leftPx + 0.3\n      const score = feature.get('score') as number\n      ctx.fillRect(leftPx, toY(score), w, toHeight(score))\n    }\n\n    // Keep track of previous total which we will use it to draw the interbase\n    // indicator (if there is a sudden clip, there will be no read coverage but\n    // there will be \"clip\" coverage) at that position beyond the read. if the\n    // clip is right at a block boundary then prevTotal will not be available,\n    // so this is a best attempt to plot interbase indicator at the \"cliffs\"\n    let prevTotal = 0\n\n    // extraHorizontallyFlippedOffset is used to draw interbase items, which\n    // are located to the left when forward and right when reversed\n    const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0\n\n    // Second pass: draw the SNP data, and add a minimum feature width of 1px\n    // which can be wider than the actual bpPerPx This reduces overdrawing of\n    // the grey background over the SNPs\n\n    for (let i = 0; i < coverage.length; i++) {\n      const feature = coverage[i]\n      const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx)\n\n      const snpinfo = feature.get('snpinfo') as SNPInfo\n      const w = Math.max(rightPx - leftPx + 0.3, 1)\n      const totalScore = snpinfo.total\n      const keys = Object.keys(snpinfo.cov).sort()\n\n      let curr = 0\n      for (let i = 0; i < keys.length; i++) {\n        const base = keys[i]\n        const { total } = snpinfo.cov[base]\n        ctx.fillStyle =\n          colorForBase[base] ||\n          modificationTagMap[base.replace('mod_', '')] ||\n          '#888'\n        ctx.fillRect(leftPx, snpToY(total + curr), w, snpToHeight(total))\n        curr += total\n      }\n\n      const interbaseEvents = Object.keys(snpinfo.noncov)\n      const indicatorHeight = 4.5\n      if (drawInterbaseCounts) {\n        let curr = 0\n        for (let i = 0; i < interbaseEvents.length; i++) {\n          const base = interbaseEvents[i]\n          const { total } = snpinfo.noncov[base]\n          ctx.fillStyle = colorForBase[base]\n          ctx.fillRect(\n            leftPx - 0.6 + extraHorizontallyFlippedOffset,\n            indicatorHeight + indicatorToHeight(curr),\n            1.2,\n            indicatorToHeight(total),\n          )\n          curr += total\n        }\n      }\n\n      if (drawIndicators) {\n        let accum = 0\n        let max = 0\n        let maxBase = ''\n        for (let i = 0; i < interbaseEvents.length; i++) {\n          const base = interbaseEvents[i]\n          const { total } = snpinfo.noncov[base]\n          accum += total\n          if (total > max) {\n            max = total\n            maxBase = base\n          }\n        }\n\n        // avoid drawing a bunch of indicators if coverage is very low e.g.\n        // less than 7, uses the prev total in the case of the \"cliff\"\n        const indicatorComparatorScore = Math.max(totalScore, prevTotal)\n        if (\n          accum > indicatorComparatorScore * indicatorThreshold &&\n          indicatorComparatorScore > 7\n        ) {\n          ctx.fillStyle = colorForBase[maxBase]\n          ctx.beginPath()\n          const l = leftPx + extraHorizontallyFlippedOffset\n          ctx.moveTo(l - 3.5, 0)\n          ctx.lineTo(l + 3.5, 0)\n          ctx.lineTo(l, indicatorHeight)\n          ctx.fill()\n        }\n      }\n      prevTotal = totalScore\n    }\n\n    if (drawArcs) {\n      for (let i = 0; i < skips.length; i++) {\n        const f = skips[i]\n        const [left, right] = bpSpanPx(\n          f.get('start'),\n          f.get('end'),\n          region,\n          bpPerPx,\n        )\n\n        ctx.beginPath()\n        const str = f.get('strand') as number\n        const xs = f.get('xs') as string\n        const pos = 'rgba(255,200,200,0.7)'\n        const neg = 'rgba(200,200,255,0.7)'\n        const neutral = 'rgba(200,200,200,0.7)'\n\n        if (xs === '+') {\n          ctx.strokeStyle = pos\n        } else if (xs === '-') {\n          ctx.strokeStyle = neg\n        } else if (str === 1) {\n          ctx.strokeStyle = pos\n        } else if (str === -1) {\n          ctx.strokeStyle = neg\n        } else {\n          ctx.strokeStyle = neutral\n        }\n\n        ctx.lineWidth = Math.log(f.get('score') + 1)\n        ctx.moveTo(left, height - offset * 2)\n        ctx.bezierCurveTo(left, 0, right, 0, right, height - offset * 2)\n        ctx.stroke()\n      }\n    }\n\n    if (displayCrossHatches) {\n      ctx.lineWidth = 1\n      ctx.strokeStyle = 'rgba(140,140,140,0.8)'\n      ticks.values.forEach(tick => {\n        ctx.beginPath()\n        ctx.moveTo(0, Math.round(toY(tick)))\n        ctx.lineTo(width, Math.round(toY(tick)))\n        ctx.stroke()\n      })\n    }\n  }\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport ConfigSchema from './configSchema'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport SNPCoverageRenderer from './SNPCoverageRenderer'\n\nimport { WiggleRendering } from '@jbrowse/plugin-wiggle'\n\nexport const configSchema = ConfigurationSchema(\n  'SNPCoverageRenderer',\n  {},\n  { baseConfiguration: ConfigSchema, explicitlyTyped: true },\n)\n\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addRendererType(\n    () =>\n      new SNPCoverageRenderer({\n        name: 'SNPCoverageRenderer',\n        ReactComponent: WiggleRendering,\n        configSchema,\n        pluginManager,\n      }),\n  )\n}\n","import { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { doesIntersect2 } from '@jbrowse/core/util/range'\nimport { Mismatch } from '../BamAdapter/MismatchParser'\n\ninterface SortObject {\n  pos: number\n  type: string\n  tag?: string\n}\nexport const sortFeature = (\n  features: Map<string, Feature>,\n  sortedBy: SortObject,\n) => {\n  const featureArray = Array.from(features.values())\n  const featuresInCenterLine: Feature[] = []\n  const featuresOutsideCenter: Feature[] = []\n  const { pos, type } = sortedBy\n\n  // only sort on features that intersect center line, append those outside post-sort\n  featureArray.forEach(innerArray => {\n    const feature = innerArray\n    const start = feature.get('start')\n    const end = feature.get('end')\n    if (doesIntersect2(pos - 1, pos, start, end)) {\n      featuresInCenterLine.push(innerArray)\n    } else {\n      featuresOutsideCenter.push(innerArray)\n    }\n  })\n\n  const isCram = featureArray.length ? featureArray[0].get('tags') : false\n  switch (type) {\n    case 'Start location': {\n      featuresInCenterLine.sort((a, b) => a.get('start') - b.get('start'))\n      break\n    }\n\n    case 'tag': {\n      const tag = sortedBy.tag as string\n      const getTag = (f: Feature, t: string) => {\n        return isCram ? f.get('tags')[t] : f.get(t)\n      }\n      const isString =\n        featuresInCenterLine[0] &&\n        typeof getTag(featuresInCenterLine[0], tag) === 'string'\n      if (isString) {\n        featuresInCenterLine.sort((a, b) =>\n          getTag(b, tag).localeCompare(getTag(a, tag)),\n        )\n      } else {\n        featuresInCenterLine.sort(\n          (a, b) => (getTag(b, tag) || 0) - (getTag(a, tag) || 0),\n        )\n      }\n      break\n    }\n\n    // first sort all mismatches, then all reference bases at the end\n    case 'Base pair': {\n      const baseSortArray: [string, Mismatch][] = []\n      featuresInCenterLine.forEach(feature => {\n        const mismatches: Mismatch[] = feature.get('mismatches')\n        mismatches.forEach(mismatch => {\n          const start = feature.get('start')\n          const offset = start + mismatch.start + 1\n          const consuming =\n            mismatch.type === 'insertion' || mismatch.type === 'softclip'\n          const len = consuming ? 0 : mismatch.length\n          if (pos >= offset && pos < offset + len) {\n            baseSortArray.push([feature.id(), mismatch])\n          }\n        })\n      })\n\n      const baseMap = new Map(baseSortArray)\n      featuresInCenterLine.sort((a, b) => {\n        const aMismatch = baseMap.get(a.id())\n        const bMismatch = baseMap.get(b.id())\n        const acode = bMismatch && bMismatch.base.toUpperCase()\n        const bcode = aMismatch && aMismatch.base.toUpperCase()\n        if (acode === bcode && acode === '*') {\n          // @ts-ignore\n          return aMismatch.length - bMismatch.length\n        }\n        return (\n          (acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0)\n        )\n      })\n\n      break\n    }\n\n    // sorts positive strands then negative strands\n    case 'Read strand': {\n      featuresInCenterLine.sort((a, b) =>\n        a.get('strand') <= b.get('strand') ? 1 : -1,\n      )\n      break\n    }\n  }\n\n  const sortedMap = new Map(\n    featuresInCenterLine\n      .concat(featuresOutsideCenter)\n      .map(feature => [feature.id(), feature]),\n  )\n\n  return sortedMap\n}\n","import deepEqual from 'fast-deep-equal'\nimport { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'\nimport SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'\nimport GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout'\nimport MultiLayout from '@jbrowse/core/util/layouts/MultiLayout'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\nexport interface PileupLayoutSessionProps {\n  config: AnyConfigurationModel\n  bpPerPx: number\n  filters: SerializableFilterChain\n  sortedBy: unknown\n  showSoftClip: unknown\n}\n\ntype MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>\ninterface CachedPileupLayout {\n  layout: MyMultiLayout\n  config: AnyConfigurationModel\n  filters: SerializableFilterChain\n  sortedBy: unknown\n  showSoftClip: boolean\n}\n// Sorting and revealing soft clip changes the layout of Pileup renderer\n// Adds extra conditions to see if cached layout is valid\nexport class PileupLayoutSession extends LayoutSession {\n  sortedBy: unknown\n\n  showSoftClip = false\n\n  constructor(args: PileupLayoutSessionProps) {\n    super(args)\n    this.config = args.config\n  }\n\n  cachedLayoutIsValid(cachedLayout: CachedPileupLayout) {\n    return (\n      super.cachedLayoutIsValid(cachedLayout) &&\n      this.showSoftClip === cachedLayout.showSoftClip &&\n      deepEqual(this.sortedBy, cachedLayout.sortedBy)\n    )\n  }\n\n  cachedLayout: CachedPileupLayout | undefined\n\n  get layout(): MyMultiLayout {\n    if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {\n      this.cachedLayout = {\n        layout: this.makeLayout(),\n        config: readConfObject(this.config),\n        filters: this.filters,\n        sortedBy: this.sortedBy,\n        showSoftClip: this.showSoftClip,\n      }\n    }\n    return this.cachedLayout.layout\n  }\n}\n","import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'\nimport { toArray } from 'rxjs/operators'\nimport BoxRendererType, {\n  RenderArgs,\n  RenderArgsSerialized,\n  RenderArgsDeserialized as BoxRenderArgsDeserialized,\n  RenderResults,\n  ResultsSerialized,\n  ResultsDeserialized,\n} from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'\nimport { Theme } from '@material-ui/core'\nimport { createJBrowseTheme } from '@jbrowse/core/ui'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { bpSpanPx, iterMap } from '@jbrowse/core/util'\nimport Color from 'color'\nimport { Region } from '@jbrowse/core/util/types'\nimport { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils'\nimport { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout'\nimport { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport { readConfObject } from '@jbrowse/core/configuration'\n\n// locals\nimport {\n  Mismatch,\n  parseCigar,\n  getModificationPositions,\n  getNextRefPos,\n} from '../BamAdapter/MismatchParser'\nimport { sortFeature } from './sortUtil'\nimport { getTagAlt, orientationTypes } from '../util'\nimport {\n  PileupLayoutSession,\n  PileupLayoutSessionProps,\n} from './PileupLayoutSession'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\n\nfunction getColorBaseMap(theme: Theme) {\n  return {\n    A: theme.palette.bases.A.main,\n    C: theme.palette.bases.C.main,\n    G: theme.palette.bases.G.main,\n    T: theme.palette.bases.T.main,\n    deletion: '#808080', // gray\n  }\n}\n\nexport interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {\n  colorBy?: { type: string; tag?: string }\n  colorTagMap?: Record<string, string>\n  modificationTagMap?: Record<string, string>\n  sortedBy?: {\n    type: string\n    pos: number\n    refName: string\n    assemblyName: string\n    tag?: string\n  }\n  showSoftClip: boolean\n  highResolutionScaling: number\n}\n\nexport interface RenderArgsDeserializedWithFeaturesAndLayout\n  extends RenderArgsDeserialized {\n  features: Map<string, Feature>\n  layout: BaseLayout<Feature>\n  regionSequence?: string\n}\n\ninterface LayoutRecord {\n  feature: Feature\n  leftPx: number\n  rightPx: number\n  topPx: number\n  heightPx: number\n}\n\nconst alignmentColoring: { [key: string]: string } = {\n  color_fwd_strand_not_proper: '#ECC8C8',\n  color_rev_strand_not_proper: '#BEBED8',\n  color_fwd_strand: '#EC8B8B',\n  color_rev_strand: '#8F8FD8',\n  color_fwd_missing_mate: '#D11919',\n  color_rev_missing_mate: '#1919D1',\n  color_fwd_diff_chr: '#000',\n  color_rev_diff_chr: '#969696',\n  color_pair_lr: '#c8c8c8',\n  color_pair_rr: 'navy',\n  color_pair_rl: 'teal',\n  color_pair_ll: 'green',\n  color_nostrand: '#c8c8c8',\n  color_interchrom: 'orange',\n  color_longinsert: 'red',\n  color_shortinsert: 'pink',\n}\n\ninterface LayoutFeature {\n  heightPx: number\n  topPx: number\n  feature: Feature\n}\n\nfunction shouldDrawMismatches(type?: string) {\n  return !['methylation', 'modifications'].includes(type || '')\n}\n\nexport default class PileupRenderer extends BoxRendererType {\n  supportsSVG = true\n\n  // get width and height of chars the height is an approximation: width\n  // letter M is approximately the height\n  getCharWidthHeight(ctx: CanvasRenderingContext2D) {\n    const charWidth = ctx.measureText('A').width\n    const charHeight = ctx.measureText('M').width\n    return { charWidth, charHeight }\n  }\n\n  layoutFeature({\n    feature,\n    layout,\n    bpPerPx,\n    region,\n    showSoftClip,\n    heightPx,\n    displayMode,\n  }: {\n    feature: Feature\n    layout: BaseLayout<Feature>\n    bpPerPx: number\n    region: Region\n    showSoftClip?: boolean\n    heightPx: number\n    displayMode: string\n  }): LayoutRecord | null {\n    let expansionBefore = 0\n    let expansionAfter = 0\n\n    // Expand the start and end of feature when softclipping enabled\n    if (showSoftClip) {\n      const mismatches = feature.get('mismatches') as Mismatch[]\n      const seq = feature.get('seq') as string\n      if (seq) {\n        for (let i = 0; i < mismatches.length; i += 1) {\n          const { type, start, cliplen = 0 } = mismatches[i]\n          if (type === 'softclip') {\n            start === 0\n              ? (expansionBefore = cliplen)\n              : (expansionAfter = cliplen)\n          }\n        }\n      }\n    }\n\n    const [leftPx, rightPx] = bpSpanPx(\n      feature.get('start') - expansionBefore,\n      feature.get('end') + expansionAfter,\n      region,\n      bpPerPx,\n    )\n\n    if (displayMode === 'compact') {\n      heightPx /= 3\n    }\n    if (feature.get('refName') !== region.refName) {\n      throw new Error(\n        `feature ${feature.id()} is not on the current region's reference sequence ${\n          region.refName\n        }`,\n      )\n    }\n    const topPx = layout.addRect(\n      feature.id(),\n      feature.get('start') - expansionBefore,\n      feature.get('end') + expansionAfter,\n      heightPx,\n    )\n    if (topPx === null) {\n      return null\n    }\n\n    return {\n      feature,\n      leftPx,\n      rightPx,\n      topPx: displayMode === 'collapse' ? 0 : topPx,\n      heightPx,\n    }\n  }\n\n  // expands region for clipping to use. possible improvement: use average read\n  // size to set the heuristic maxClippingSize expansion (e.g. short reads\n  // don't have to expand a softclipping size a lot, but long reads might)\n  getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized) {\n    const { config, showSoftClip } = renderArgs\n\n    const maxClippingSize = readConfObject(config, 'maxClippingSize')\n    const { start, end } = region\n    const len = end - start\n    const bpExpansion = Math.max(\n      len,\n      showSoftClip ? Math.round(maxClippingSize) : 0,\n    )\n\n    return {\n      ...region,\n      start: Math.floor(Math.max(start - bpExpansion, 0)),\n      end: Math.ceil(end + bpExpansion),\n    }\n  }\n\n  colorByOrientation(feature: Feature, config: AnyConfigurationModel) {\n    return alignmentColoring[\n      this.getOrientation(feature, config) || 'color_nostrand'\n    ]\n  }\n\n  getOrientation(feature: Feature, config: AnyConfigurationModel) {\n    const orientationType = readConfObject(config, 'orientationType') as\n      | 'fr'\n      | 'ff'\n      | 'rf'\n    const type = orientationTypes[orientationType]\n    const orientation = type[feature.get('pair_orientation') as string]\n    const map: { [key: string]: string } = {\n      LR: 'color_pair_lr',\n      RR: 'color_pair_rr',\n      RL: 'color_pair_rl',\n      LL: 'color_pair_ll',\n    }\n    return map[orientation]\n  }\n\n  colorByInsertSize(feature: Feature, _config: AnyConfigurationModel) {\n    return feature.get('is_paired') &&\n      feature.get('seq_id') !== feature.get('next_seq_id')\n      ? '#555'\n      : `hsl(${Math.abs(feature.get('template_length')) / 10},50%,50%)`\n  }\n\n  colorByStranded(feature: Feature, _config: AnyConfigurationModel) {\n    const flags = feature.get('flags')\n    const strand = feature.get('strand')\n    // is paired\n    if (flags & 1) {\n      const revflag = flags & 64\n      const flipper = revflag ? -1 : 1\n      // proper pairing\n      if (flags & 2) {\n        return strand * flipper === 1 ? 'color_rev_strand' : 'color_fwd_strand'\n      }\n      if (feature.get('multi_segment_next_segment_unmapped')) {\n        return strand * flipper === 1\n          ? 'color_rev_missing_mate'\n          : 'color_fwd_missing_mate'\n      }\n      if (feature.get('seq_id') === feature.get('next_seq_id')) {\n        return strand * flipper === 1\n          ? 'color_rev_strand_not_proper'\n          : 'color_fwd_strand_not_proper'\n      }\n      // should only leave aberrant chr\n      return strand === 1 ? 'color_fwd_diff_chr' : 'color_rev_diff_chr'\n    }\n    return strand === 1 ? 'color_fwd_strand' : 'color_rev_strand'\n  }\n\n  colorByPerBaseQuality(\n    ctx: CanvasRenderingContext2D,\n    feat: LayoutFeature,\n    _config: AnyConfigurationModel,\n    region: Region,\n    bpPerPx: number,\n  ) {\n    const { feature, topPx, heightPx } = feat\n    const qual: string = feature.get('qual') || ''\n    const scores = qual.split(' ').map(val => +val)\n    const cigarOps = parseCigar(feature.get('CIGAR'))\n    const width = 1 / bpPerPx\n    const start = feature.get('start')\n\n    for (let i = 0, j = 0, k = 0; k < scores.length; i += 2, k++) {\n      const len = +cigarOps[i]\n      const op = cigarOps[i + 1]\n      if (op === 'S' || op === 'I') {\n        k += len\n      } else if (op === 'D' || op === 'N') {\n        j += len\n      } else if (op === 'M' || op === 'X' || op === '=') {\n        for (let m = 0; m < len; m++) {\n          const score = scores[k + m]\n          ctx.fillStyle = `hsl(${score === 255 ? 150 : score * 1.5},55%,50%)`\n          const [leftPx] = bpSpanPx(\n            start + j + m,\n            start + j + m + 1,\n            region,\n            bpPerPx,\n          )\n          ctx.fillRect(leftPx, topPx, width + 0.5, heightPx)\n        }\n        j += len\n      }\n    }\n  }\n\n  // ML stores probabilities as array of numerics and MP is scaled phred scores\n  // https://github.com/samtools/hts-specs/pull/418/files#diff-e765c6479316309f56b636f88189cdde8c40b854c7bdcce9ee7fe87a4e76febcR596\n  //\n  // if we have ML or Ml, it is an 8bit probability, divide by 255\n  //\n  // if we have MP or Mp it is phred scaled ASCII, which can go up to 90 but\n  // has very high likelihood basecalls at that point, we really only care\n  // about low qual calls <20 approx\n  //\n  colorByModifications(\n    ctx: CanvasRenderingContext2D,\n    layoutFeature: LayoutFeature,\n    _config: AnyConfigurationModel,\n    region: Region,\n    bpPerPx: number,\n    props: RenderArgsDeserializedWithFeaturesAndLayout,\n  ) {\n    const { feature, topPx, heightPx } = layoutFeature\n    const { modificationTagMap = {} } = props\n\n    const mm = (getTagAlt(feature, 'MM', 'Mm') as string) || ''\n\n    const ml = (getTagAlt(feature, 'ML', 'Ml') as number[] | string) || []\n\n    const probabilities = ml\n      ? (typeof ml === 'string' ? ml.split(',').map(e => +e) : ml).map(\n          e => e / 255,\n        )\n      : (getTagAlt(feature, 'MP', 'Mp') as string)\n          .split('')\n          .map(s => s.charCodeAt(0) - 33)\n          .map(elt => Math.min(1, elt / 50))\n\n    const cigar = feature.get('CIGAR')\n    const start = feature.get('start')\n    const end = feature.get('end')\n    const seq = feature.get('seq')\n    const strand = feature.get('strand')\n    const cigarOps = parseCigar(cigar)\n\n    const modifications = getModificationPositions(mm, seq, strand)\n\n    // probIndex applies across multiple modifications e.g.\n    let probIndex = 0\n    for (let i = 0; i < modifications.length; i++) {\n      const { type, positions } = modifications[i]\n      const col = modificationTagMap[type] || 'black'\n      const base = Color(col)\n      for (const readPos of getNextRefPos(cigarOps, positions)) {\n        if (readPos >= 0 && start + readPos < end) {\n          const [leftPx, rightPx] = bpSpanPx(\n            start + readPos,\n            start + readPos + 1,\n            region,\n            bpPerPx,\n          )\n\n          // give it a little boost of 0.1 to not make them fully\n          // invisible to avoid confusion\n          ctx.fillStyle = base\n            .alpha(probabilities[probIndex] + 0.1)\n            .hsl()\n            .string()\n          ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx)\n        }\n        probIndex++\n      }\n    }\n  }\n\n  // Color by methylation is slightly modified version of color by\n  // modifications\n  //\n  colorByMethylation(\n    ctx: CanvasRenderingContext2D,\n    layoutFeature: LayoutFeature,\n    _config: AnyConfigurationModel,\n    region: Region,\n    bpPerPx: number,\n    props: RenderArgsDeserializedWithFeaturesAndLayout,\n  ) {\n    const { regionSequence } = props\n    const { feature, topPx, heightPx } = layoutFeature\n\n    const mm: string = getTagAlt(feature, 'MM', 'Mm') || ''\n\n    if (!regionSequence) {\n      throw new Error('region sequence required for methylation')\n    }\n\n    const cigar = feature.get('CIGAR')\n    const fstart = feature.get('start')\n    const fend = feature.get('end')\n    const seq = feature.get('seq')\n    const strand = feature.get('strand')\n    const cigarOps = parseCigar(cigar)\n    const { start: rstart, end: rend } = region\n\n    const methBins = new Array(rend - rstart).fill(0)\n    const modifications = getModificationPositions(mm, seq, strand)\n    for (let i = 0; i < modifications.length; i++) {\n      const { type, positions } = modifications[i]\n      if (type === 'm' && positions) {\n        for (const pos of getNextRefPos(cigarOps, positions)) {\n          const epos = pos + fstart - rstart\n          if (epos >= 0 && epos < methBins.length) {\n            methBins[epos] = 1\n          }\n        }\n      }\n    }\n\n    for (let j = fstart; j < fend; j++) {\n      const i = j - rstart\n      if (i >= 0 && i < methBins.length) {\n        const l1 = regionSequence[i].toLowerCase()\n        const l2 = regionSequence[i + 1].toLowerCase()\n\n        // if we are zoomed out, display just a block over the cpg\n        if (bpPerPx > 2) {\n          if (l1 === 'c' && l2 === 'g') {\n            const s = rstart + i\n            const [leftPx, rightPx] = bpSpanPx(s, s + 2, region, bpPerPx)\n            if (methBins[i] || methBins[i + 1]) {\n              ctx.fillStyle = 'red'\n            } else {\n              ctx.fillStyle = 'blue'\n            }\n            ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx)\n          }\n        }\n        // if we are zoomed in, color the c inside the cpg\n        else {\n          // color\n          if (l1 === 'c' && l2 === 'g') {\n            const s = rstart + i\n            const [leftPx, rightPx] = bpSpanPx(s, s + 1, region, bpPerPx)\n            if (methBins[i]) {\n              ctx.fillStyle = 'red'\n            } else {\n              ctx.fillStyle = 'blue'\n            }\n            ctx.fillRect(leftPx, topPx, rightPx - leftPx + 0.5, heightPx)\n\n            const [leftPx2, rightPx2] = bpSpanPx(s + 1, s + 2, region, bpPerPx)\n            if (methBins[i + 1]) {\n              ctx.fillStyle = 'red'\n            } else {\n              ctx.fillStyle = 'blue'\n            }\n            ctx.fillRect(leftPx2, topPx, rightPx2 - leftPx2 + 0.5, heightPx)\n          }\n        }\n      }\n    }\n  }\n\n  drawRect(\n    ctx: CanvasRenderingContext2D,\n    feat: LayoutFeature,\n    props: RenderArgsDeserialized,\n  ) {\n    const { regions, bpPerPx } = props\n    const { heightPx, topPx, feature } = feat\n    const [region] = regions\n    const [leftPx, rightPx] = bpSpanPx(\n      feature.get('start'),\n      feature.get('end'),\n      region,\n      bpPerPx,\n    )\n    const flip = region.reversed ? -1 : 1\n    const strand = feature.get('strand') * flip\n    if (bpPerPx < 10) {\n      if (strand === -1) {\n        ctx.beginPath()\n        ctx.moveTo(leftPx - 5, topPx + heightPx / 2)\n        ctx.lineTo(leftPx, topPx + heightPx)\n        ctx.lineTo(rightPx, topPx + heightPx)\n        ctx.lineTo(rightPx, topPx)\n        ctx.lineTo(leftPx, topPx)\n        ctx.closePath()\n        ctx.fill()\n      } else {\n        ctx.beginPath()\n        ctx.moveTo(leftPx, topPx)\n        ctx.lineTo(leftPx, topPx + heightPx)\n        ctx.lineTo(rightPx, topPx + heightPx)\n        ctx.lineTo(rightPx + 5, topPx + heightPx / 2)\n        ctx.lineTo(rightPx, topPx)\n        ctx.closePath()\n        ctx.fill()\n      }\n    } else {\n      ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx)\n    }\n  }\n\n  drawAlignmentRect(\n    ctx: CanvasRenderingContext2D,\n    feat: LayoutFeature,\n    props: RenderArgsDeserializedWithFeaturesAndLayout & {\n      defaultColor: boolean\n    },\n  ) {\n    const {\n      defaultColor,\n      config,\n      bpPerPx,\n      regions,\n      colorBy,\n      colorTagMap = {},\n    } = props\n    const { tag = '', type: colorType = '' } = colorBy || {}\n    const { feature } = feat\n    const region = regions[0]\n\n    // first pass for simple color changes that change the color of the\n    // alignment\n    switch (colorType) {\n      case 'insertSize':\n        ctx.fillStyle = this.colorByInsertSize(feature, config)\n        break\n      case 'strand':\n        ctx.fillStyle = feature.get('strand') === -1 ? '#8F8FD8' : '#EC8B8B'\n        break\n      case 'mappingQuality':\n        ctx.fillStyle = `hsl(${feature.get('mq')},50%,50%)`\n        break\n\n      case 'pairOrientation':\n        ctx.fillStyle = this.colorByOrientation(feature, config)\n        break\n      case 'stranded':\n        ctx.fillStyle = alignmentColoring[this.colorByStranded(feature, config)]\n        break\n      case 'xs':\n      case 'tag': {\n        const tags = feature.get('tags')\n        const val = tags ? tags[tag] : feature.get(tag)\n\n        // special for for XS/TS tag\n        if (tag === 'XS' || tag === 'TS') {\n          const map: { [key: string]: string | undefined } = {\n            '-': 'color_rev_strand',\n            '+': 'color_fwd_strand',\n          }\n          ctx.fillStyle = alignmentColoring[map[val] || 'color_nostrand']\n        }\n\n        // lower case 'ts' from minimap2 is flipped from xs\n        if (tag === 'ts') {\n          const map: { [key: string]: string } = {\n            '-':\n              feature.get('strand') === -1\n                ? 'color_fwd_strand'\n                : 'color_rev_strand',\n            '+':\n              feature.get('strand') === -1\n                ? 'color_rev_strand'\n                : 'color_fwd_strand',\n          }\n          ctx.fillStyle = alignmentColoring[map[val] || 'color_nostrand']\n        }\n\n        // tag is not one of the autofilled tags, has color-value pairs from\n        // fetchValues\n        else {\n          const foundValue = colorTagMap[val]\n          ctx.fillStyle = foundValue || alignmentColoring['color_nostrand']\n        }\n        break\n      }\n      case 'insertSizeAndPairOrientation':\n        break\n\n      case 'normal':\n      default:\n        if (defaultColor) {\n          // avoid a readConfObject call here\n          ctx.fillStyle = '#c8c8c8'\n        } else {\n          ctx.fillStyle = readConfObject(config, 'color', { feature })\n        }\n        break\n    }\n\n    this.drawRect(ctx, feat, props)\n\n    // second pass for color types that render per-base things that go over the\n    // existing drawing\n    switch (colorType) {\n      case 'perBaseQuality':\n        this.colorByPerBaseQuality(ctx, feat, config, region, bpPerPx)\n        break\n\n      case 'modifications':\n        this.colorByModifications(ctx, feat, config, region, bpPerPx, props)\n        break\n\n      case 'methylation':\n        this.colorByMethylation(ctx, feat, config, region, bpPerPx, props)\n        break\n    }\n  }\n\n  drawMismatches(\n    ctx: CanvasRenderingContext2D,\n    feat: LayoutFeature,\n    props: RenderArgsDeserializedWithFeaturesAndLayout,\n    theme: Theme,\n    colorForBase: { [key: string]: string },\n    opts: {\n      mismatchAlpha?: boolean\n      drawSNPs?: boolean\n      drawIndels?: boolean\n      minSubfeatureWidth: number\n      largeInsertionIndicatorScale: number\n      charWidth: number\n      charHeight: number\n    },\n  ) {\n    const {\n      minSubfeatureWidth: minWidth,\n      largeInsertionIndicatorScale,\n      mismatchAlpha,\n      drawSNPs = true,\n      drawIndels = true,\n      charWidth,\n      charHeight,\n    } = opts\n    const { bpPerPx, regions } = props\n    const { heightPx, topPx, feature } = feat\n    const [region] = regions\n    const start = feature.get('start')\n\n    const pxPerBp = Math.min(1 / bpPerPx, 2)\n    const w = Math.max(minWidth, pxPerBp)\n    const mismatches: Mismatch[] = feature.get('mismatches')\n    const heightLim = charHeight - 2\n\n    function getAlphaColor(baseColor: string, mismatch: { qual?: number }) {\n      let color = baseColor\n      if (mismatchAlpha && mismatch.qual !== undefined) {\n        color = Color(baseColor)\n          .alpha(Math.min(1, mismatch.qual / 50))\n          .hsl()\n          .string()\n      }\n      return color\n    }\n\n    // extraHorizontallyFlippedOffset is used to draw interbase items, which\n    // are located to the left when forward and right when reversed\n    const extraHorizontallyFlippedOffset = region.reversed\n      ? 1 / bpPerPx + 1\n      : -1\n\n    // two pass rendering: first pass, draw all the mismatches except wide\n    // insertion markers\n    for (let i = 0; i < mismatches.length; i += 1) {\n      const mismatch = mismatches[i]\n      const mstart = start + mismatch.start\n      const mlen = mismatch.length\n      const mbase = mismatch.base\n      const [leftPx, rightPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx)\n      const widthPx = Math.max(minWidth, Math.abs(leftPx - rightPx))\n      if (mismatch.type === 'mismatch' && drawSNPs) {\n        const baseColor = colorForBase[mismatch.base] || '#888'\n\n        ctx.fillStyle = getAlphaColor(baseColor, mismatch)\n\n        ctx.fillRect(leftPx, topPx, widthPx, heightPx)\n\n        if (widthPx >= charWidth && heightPx >= heightLim) {\n          // normal SNP coloring\n          ctx.fillStyle = getAlphaColor(\n            theme.palette.getContrastText(baseColor),\n            mismatch,\n          )\n          ctx.fillText(\n            mbase,\n            leftPx + (widthPx - charWidth) / 2 + 1,\n            topPx + heightPx,\n          )\n        }\n      } else if (mismatch.type === 'deletion' && drawIndels) {\n        const baseColor = colorForBase.deletion\n        ctx.fillStyle = baseColor\n        ctx.fillRect(leftPx, topPx, widthPx, heightPx)\n        const txt = `${mismatch.length}`\n        const rect = ctx.measureText(txt)\n        if (widthPx >= rect.width && heightPx >= heightLim) {\n          ctx.fillStyle = theme.palette.getContrastText(baseColor)\n          ctx.fillText(\n            txt,\n            leftPx + (rightPx - leftPx) / 2 - rect.width / 2,\n            topPx + heightPx,\n          )\n        }\n      } else if (mismatch.type === 'insertion' && drawIndels) {\n        ctx.fillStyle = 'purple'\n        const pos = leftPx + extraHorizontallyFlippedOffset\n        const len = +mismatch.base || mismatch.length\n        const insW = Math.max(minWidth, Math.min(1.2, 1 / bpPerPx))\n        if (len < 10) {\n          ctx.fillRect(pos, topPx, insW, heightPx)\n          if (1 / bpPerPx >= charWidth) {\n            ctx.fillRect(pos - insW, topPx, insW * 3, 1)\n            ctx.fillRect(pos - insW, topPx + heightPx - 1, insW * 3, 1)\n          }\n          if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {\n            ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx)\n          }\n        }\n      } else if (mismatch.type === 'hardclip' || mismatch.type === 'softclip') {\n        ctx.fillStyle = mismatch.type === 'hardclip' ? 'red' : 'blue'\n        const pos = leftPx + extraHorizontallyFlippedOffset\n        ctx.fillRect(pos, topPx, w, heightPx)\n        if (1 / bpPerPx >= charWidth) {\n          ctx.fillRect(pos - w, topPx, w * 3, 1)\n          ctx.fillRect(pos - w, topPx + heightPx - 1, w * 3, 1)\n        }\n        if (widthPx >= charWidth && heightPx >= heightLim) {\n          ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx)\n        }\n      } else if (mismatch.type === 'skip') {\n        // fix to avoid bad rendering note that this was also related to chrome\n        // bug https://bugs.chromium.org/p/chromium/issues/detail?id=1131528\n        // also affected firefox ref #1236 #2750\n        if (leftPx + widthPx > 0) {\n          // make small exons more visible when zoomed far out\n          const adjustPx = widthPx - (bpPerPx > 10 ? 1.5 : 0)\n          ctx.clearRect(leftPx, topPx, adjustPx, heightPx)\n          ctx.fillStyle = '#333'\n          ctx.fillRect(\n            Math.max(0, leftPx),\n            topPx + heightPx / 2 - 1,\n            adjustPx + (leftPx < 0 ? leftPx : 0),\n            2,\n          )\n        }\n      }\n    }\n\n    // second pass, draw wide insertion markers on top\n    if (drawIndels) {\n      for (let i = 0; i < mismatches.length; i += 1) {\n        const mismatch = mismatches[i]\n        const mstart = start + mismatch.start\n        const mlen = mismatch.length\n        const [leftPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx)\n        const len = +mismatch.base || mismatch.length\n        const txt = `${len}`\n        if (mismatch.type === 'insertion' && len >= 10) {\n          if (bpPerPx > largeInsertionIndicatorScale) {\n            ctx.fillStyle = 'purple'\n            ctx.fillRect(leftPx - 1, topPx, 2, heightPx)\n          } else if (heightPx > charHeight) {\n            const rect = ctx.measureText(txt)\n            const padding = 5\n            ctx.fillStyle = 'purple'\n            ctx.fillRect(\n              leftPx - rect.width / 2 - padding,\n              topPx,\n              rect.width + 2 * padding,\n              heightPx,\n            )\n            ctx.fillStyle = 'white'\n            ctx.fillText(txt, leftPx - rect.width / 2, topPx + heightPx)\n          } else {\n            const padding = 2\n            ctx.fillStyle = 'purple'\n            ctx.fillRect(leftPx - padding, topPx, 2 * padding, heightPx)\n          }\n        }\n      }\n    }\n  }\n\n  drawSoftClipping(\n    ctx: CanvasRenderingContext2D,\n    feat: LayoutFeature,\n    props: RenderArgsDeserializedWithFeaturesAndLayout,\n    config: AnyConfigurationModel,\n    theme: Theme,\n  ) {\n    const { feature, topPx, heightPx } = feat\n    const { regions, bpPerPx } = props\n    const [region] = regions\n    const minFeatWidth = readConfObject(config, 'minSubfeatureWidth')\n    const mismatches: Mismatch[] = feature.get('mismatches')\n    const seq = feature.get('seq')\n    const { charWidth, charHeight } = this.getCharWidthHeight(ctx)\n    const colorForBase: { [key: string]: string } = {\n      A: theme.palette.bases.A.main,\n      C: theme.palette.bases.C.main,\n      G: theme.palette.bases.G.main,\n      T: theme.palette.bases.T.main,\n      deletion: '#808080', // gray\n    }\n\n    // Display all bases softclipped off in lightened colors\n    if (seq) {\n      mismatches\n        .filter(mismatch => mismatch.type === 'softclip')\n        .forEach(mismatch => {\n          const softClipLength = mismatch.cliplen || 0\n          const s = feature.get('start')\n          const softClipStart =\n            mismatch.start === 0 ? s - softClipLength : s + mismatch.start\n\n          for (let k = 0; k < softClipLength; k += 1) {\n            const base = seq.charAt(k + mismatch.start)\n\n            // If softclip length+start is longer than sequence, no need to\n            // continue showing base\n            if (!base) {\n              return\n            }\n\n            const [softClipLeftPx, softClipRightPx] = bpSpanPx(\n              softClipStart + k,\n              softClipStart + k + 1,\n              region,\n              bpPerPx,\n            )\n            const softClipWidthPx = Math.max(\n              minFeatWidth,\n              Math.abs(softClipLeftPx - softClipRightPx),\n            )\n\n            // Black accounts for IUPAC ambiguity code bases such as N that\n            // show in soft clipping\n            const baseColor = colorForBase[base] || '#000000'\n            ctx.fillStyle = baseColor\n            ctx.fillRect(softClipLeftPx, topPx, softClipWidthPx, heightPx)\n\n            if (softClipWidthPx >= charWidth && heightPx >= charHeight - 5) {\n              ctx.fillStyle = theme.palette.getContrastText(baseColor)\n              ctx.fillText(\n                base,\n                softClipLeftPx + (softClipWidthPx - charWidth) / 2 + 1,\n                topPx + heightPx,\n              )\n            }\n          }\n        })\n    }\n  }\n\n  async makeImageData(\n    ctx: CanvasRenderingContext2D,\n    layoutRecords: (LayoutFeature | null)[],\n    props: RenderArgsDeserializedWithFeaturesAndLayout,\n  ) {\n    const { layout, config, showSoftClip, colorBy, theme: configTheme } = props\n    const mismatchAlpha = readConfObject(config, 'mismatchAlpha')\n    const minSubfeatureWidth = readConfObject(config, 'minSubfeatureWidth')\n    const insertScale = readConfObject(config, 'largeInsertionIndicatorScale')\n    const defaultColor = readConfObject(config, 'color') === '#f0f'\n\n    const theme = createJBrowseTheme(configTheme)\n    const colorForBase = getColorBaseMap(theme)\n    if (!layout) {\n      throw new Error(`layout required`)\n    }\n    if (!layout.addRect) {\n      throw new Error('invalid layout object')\n    }\n    ctx.font = 'bold 10px Courier New,monospace'\n\n    const { charWidth, charHeight } = this.getCharWidthHeight(ctx)\n    layoutRecords.forEach(feat => {\n      if (feat === null) {\n        return\n      }\n\n      this.drawAlignmentRect(ctx, feat, {\n        ...props,\n        defaultColor,\n      })\n      this.drawMismatches(ctx, feat, props, theme, colorForBase, {\n        mismatchAlpha,\n        drawSNPs: shouldDrawMismatches(colorBy?.type),\n        drawIndels: shouldDrawMismatches(colorBy?.type),\n        largeInsertionIndicatorScale: insertScale,\n        minSubfeatureWidth,\n        charWidth,\n        charHeight,\n      })\n      if (showSoftClip) {\n        this.drawSoftClipping(ctx, feat, props, config, theme)\n      }\n    })\n  }\n\n  // we perform a full layout before render as a separate method because the\n  // layout determines the height of the canvas that we use to render\n  layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout) {\n    const {\n      layout,\n      features,\n      sortedBy,\n      config,\n      bpPerPx,\n      showSoftClip,\n      regions,\n    } = props\n    const [region] = regions\n    if (!layout) {\n      throw new Error(`layout required`)\n    }\n    if (!layout.addRect) {\n      throw new Error('invalid layout object')\n    }\n\n    const featureMap =\n      sortedBy?.type && region.start === sortedBy.pos\n        ? sortFeature(features, sortedBy)\n        : features\n\n    const heightPx = readConfObject(config, 'height')\n    const displayMode = readConfObject(config, 'displayMode')\n    const layoutRecords = iterMap(\n      featureMap.values(),\n      feature =>\n        this.layoutFeature({\n          feature,\n          layout,\n          bpPerPx,\n          region,\n          showSoftClip,\n          heightPx,\n          displayMode,\n        }),\n      featureMap.size,\n    )\n    return layoutRecords\n  }\n\n  async render(renderProps: RenderArgsDeserialized) {\n    const { sessionId, bpPerPx, regions, adapterConfig } = renderProps\n    const { sequenceAdapter } = adapterConfig\n    const features = await this.getFeatures(renderProps)\n    const layout = this.createLayoutInWorker(renderProps)\n\n    const layoutRecords = this.layoutFeats({ ...renderProps, features, layout })\n    const [region] = regions\n    let regionSequence: string | undefined\n    const { end, start, originalRefName, refName } = region\n\n    if (sequenceAdapter) {\n      const { dataAdapter } = await getAdapter(\n        this.pluginManager,\n        sessionId,\n        sequenceAdapter,\n      )\n\n      const feats = await (dataAdapter as BaseFeatureDataAdapter)\n        .getFeatures({\n          ...region,\n          refName: originalRefName || refName,\n          end: region.end + 1,\n        })\n        .pipe(toArray())\n        .toPromise()\n      regionSequence = feats[0]?.get('seq')\n    }\n\n    const width = (end - start) / bpPerPx\n    const height = Math.max(layout.getTotalHeight(), 1)\n\n    const res = await renderToAbstractCanvas(\n      width,\n      height,\n      renderProps,\n      (ctx: CanvasRenderingContext2D) =>\n        this.makeImageData(ctx, layoutRecords, {\n          ...renderProps,\n          layout,\n          features,\n          regionSequence,\n        }),\n    )\n\n    const results = await super.render({\n      ...renderProps,\n      ...res,\n      features,\n      layout,\n      height,\n      width,\n    })\n\n    return {\n      ...results,\n      ...res,\n      features,\n      layout,\n      height,\n      width,\n      maxHeightReached: layout.maxHeightReached,\n    }\n  }\n\n  createSession(args: PileupLayoutSessionProps) {\n    return new PileupLayoutSession(args)\n  }\n}\n\nexport type {\n  RenderArgs,\n  RenderArgsSerialized,\n  RenderResults,\n  ResultsSerialized,\n  ResultsDeserialized,\n}\n","import { Region } from '@jbrowse/core/util/types'\nimport { PrerenderedCanvas } from '@jbrowse/core/ui'\nimport { bpSpanPx } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\nimport React, { MouseEvent, useRef, useState, useEffect } from 'react'\nimport type { BaseLinearDisplayModel } from '@jbrowse/plugin-linear-genome-view'\n\n// used so that user can click-away-from-feature below the laid out features\n// (issue #1248)\nconst canvasPadding = 100\nfunction PileupRendering(props: {\n  blockKey: string\n  displayModel: BaseLinearDisplayModel\n  width: number\n  height: number\n  regions: Region[]\n  bpPerPx: number\n  sortedBy?: { type: string; pos: number; refName: string }\n  colorBy?: { type: string; tag?: string }\n  onMouseMove?: (event: React.MouseEvent, featureId: string | undefined) => void\n}) {\n  const {\n    onMouseMove,\n    blockKey,\n    displayModel,\n    width,\n    height,\n    regions,\n    bpPerPx,\n    sortedBy,\n    colorBy,\n  } = props\n  const { selectedFeatureId, featureIdUnderMouse, contextMenuFeature } =\n    displayModel\n\n  const [region] = regions\n  const highlightOverlayCanvas = useRef<HTMLCanvasElement>(null)\n  const [mouseIsDown, setMouseIsDown] = useState(false)\n  const [movedDuringLastMouseDown, setMovedDuringLastMouseDown] =\n    useState(false)\n  useEffect(() => {\n    const canvas = highlightOverlayCanvas.current\n    if (!canvas) {\n      return\n    }\n    const ctx = canvas.getContext('2d')\n    if (!ctx) {\n      return\n    }\n    ctx.clearRect(0, 0, canvas.width, canvas.height)\n    const selectedRect = selectedFeatureId\n      ? displayModel.getFeatureByID?.(blockKey, selectedFeatureId)\n      : undefined\n    if (selectedRect) {\n      const [leftBp, topPx, rightBp, bottomPx] = selectedRect\n      const [leftPx, rightPx] = bpSpanPx(leftBp, rightBp, region, bpPerPx)\n      const rectTop = Math.round(topPx)\n      const rectHeight = Math.round(bottomPx - topPx)\n      ctx.shadowColor = '#222266'\n      ctx.shadowBlur = 10\n      ctx.lineJoin = 'bevel'\n      ctx.lineWidth = 2\n      ctx.strokeStyle = '#00b8ff'\n      ctx.strokeRect(\n        leftPx - 2,\n        rectTop - 2,\n        rightPx - leftPx + 4,\n        rectHeight + 4,\n      )\n      ctx.clearRect(leftPx, rectTop, rightPx - leftPx, rectHeight)\n    }\n    const highlightedFeature = featureIdUnderMouse || contextMenuFeature?.id()\n    const highlightedRect = highlightedFeature\n      ? displayModel.getFeatureByID?.(blockKey, highlightedFeature)\n      : undefined\n    if (highlightedRect) {\n      const [leftBp, topPx, rightBp, bottomPx] = highlightedRect\n      const [leftPx, rightPx] = bpSpanPx(leftBp, rightBp, region, bpPerPx)\n      const rectTop = Math.round(topPx)\n      const rectHeight = Math.round(bottomPx - topPx)\n      ctx.fillStyle = '#0003'\n      ctx.fillRect(leftPx, rectTop, rightPx - leftPx, rectHeight)\n    }\n  }, [\n    bpPerPx,\n    region,\n    blockKey,\n    selectedFeatureId,\n    displayModel,\n    featureIdUnderMouse,\n    contextMenuFeature,\n  ])\n\n  function onMouseDown(event: MouseEvent) {\n    setMouseIsDown(true)\n    setMovedDuringLastMouseDown(false)\n    callMouseHandler('MouseDown', event)\n  }\n\n  function onMouseEnter(event: MouseEvent) {\n    callMouseHandler('MouseEnter', event)\n  }\n\n  function onMouseOut(event: MouseEvent) {\n    callMouseHandler('MouseOut', event)\n    callMouseHandler('MouseLeave', event)\n  }\n\n  function onMouseOver(event: MouseEvent) {\n    callMouseHandler('MouseOver', event)\n  }\n\n  function onMouseUp(event: MouseEvent) {\n    setMouseIsDown(false)\n    callMouseHandler('MouseUp', event)\n  }\n\n  function onClick(event: MouseEvent) {\n    if (!movedDuringLastMouseDown) {\n      callMouseHandler('Click', event)\n    }\n  }\n\n  function onMouseLeave(event: MouseEvent) {\n    callMouseHandler('MouseOut', event)\n    callMouseHandler('MouseLeave', event)\n  }\n\n  function onContextMenu(event: MouseEvent) {\n    callMouseHandler('ContextMenu', event)\n  }\n\n  function mouseMove(event: MouseEvent) {\n    if (mouseIsDown) {\n      setMovedDuringLastMouseDown(true)\n    }\n    let offsetX = 0\n    let offsetY = 0\n    const canvas = highlightOverlayCanvas.current\n    if (canvas) {\n      const { left, top } = canvas.getBoundingClientRect()\n      offsetX = left\n      offsetY = top\n    }\n    offsetX = event.clientX - offsetX\n    offsetY = event.clientY - offsetY\n    const px = region.reversed ? width - offsetX : offsetX\n    const clientBp = region.start + bpPerPx * px\n\n    const featIdUnderMouse = displayModel.getFeatureOverlapping(\n      blockKey,\n      clientBp,\n      offsetY,\n    )\n\n    if (onMouseMove) {\n      onMouseMove(event, featIdUnderMouse)\n    }\n  }\n\n  function callMouseHandler(handlerName: string, event: MouseEvent) {\n    // @ts-ignore\n    // eslint-disable-next-line react/destructuring-assignment\n    const featureHandler = props[`onFeature${handlerName}`]\n    // @ts-ignore\n    // eslint-disable-next-line react/destructuring-assignment\n    const canvasHandler = props[`on${handlerName}`]\n    if (featureHandler && featureIdUnderMouse) {\n      featureHandler(event, featureIdUnderMouse)\n    } else if (canvasHandler) {\n      canvasHandler(event, featureIdUnderMouse)\n    }\n  }\n\n  const canvasWidth = Math.ceil(width)\n  // need to call this in render so we get the right observer behavior\n  return (\n    <div\n      className=\"PileupRendering\"\n      data-testid={`pileup-${\n        sortedBy || colorBy\n          ? `${sortedBy?.type || ''}${colorBy?.type || ''}${colorBy?.tag || ''}`\n          : 'normal'\n      }`}\n      style={{ position: 'relative', width: canvasWidth, height }}\n    >\n      <PrerenderedCanvas\n        {...props}\n        style={{ position: 'absolute', left: 0, top: 0 }}\n      />\n      <canvas\n        data-testid=\"pileup_overlay_canvas\"\n        width={canvasWidth}\n        height={height + canvasPadding}\n        style={{ position: 'absolute', left: 0, top: 0 }}\n        className=\"highlightOverlayCanvas\"\n        ref={highlightOverlayCanvas}\n        onMouseDown={event => onMouseDown(event)}\n        onMouseEnter={event => onMouseEnter(event)}\n        onMouseOut={event => onMouseOut(event)}\n        onMouseOver={event => onMouseOver(event)}\n        onMouseUp={event => onMouseUp(event)}\n        onMouseLeave={event => onMouseLeave(event)}\n        onMouseMove={event => mouseMove(event)}\n        onClick={event => onClick(event)}\n        onContextMenu={event => onContextMenu(event)}\n        onFocus={() => {}}\n        onBlur={() => {}}\n      />\n    </div>\n  )\n}\n\nexport default observer(PileupRendering)\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { types } from 'mobx-state-tree'\n\nexport default ConfigurationSchema(\n  'PileupRenderer',\n  {\n    // default magenta here is used to detect the user has not customized this\n    color: {\n      type: 'color',\n      description: 'the color of each feature in a pileup alignment',\n      defaultValue: '#f0f',\n      contextVariable: ['feature'],\n    },\n    orientationType: {\n      type: 'stringEnum',\n      model: types.enumeration('orientationType', ['fr', 'rf', 'ff']),\n      defaultValue: 'fr',\n      description:\n        'read sequencer orienation. fr is normal \"reads pointing at each other ---> <--- while some other sequencers can use other options',\n    },\n    displayMode: {\n      type: 'stringEnum',\n      model: types.enumeration('displayMode', [\n        'normal',\n        'compact',\n        'collapse',\n      ]),\n      description: 'Alternative display modes',\n      defaultValue: 'normal',\n    },\n    minSubfeatureWidth: {\n      type: 'number',\n      description:\n        'the minimum width in px for a pileup mismatch feature. use for increasing mismatch marker widths when zoomed out to e.g. 1px or 0.5px',\n      defaultValue: 0,\n    },\n    maxHeight: {\n      type: 'integer',\n      description: 'the maximum height to be used in a pileup rendering',\n      defaultValue: 1200,\n    },\n    maxClippingSize: {\n      type: 'integer',\n      description: 'the max clip size to be used in a pileup rendering',\n      defaultValue: 10000,\n    },\n    height: {\n      type: 'number',\n      description: 'the height of each feature in a pileup alignment',\n      defaultValue: 7,\n      contextVariable: ['feature'],\n    },\n    noSpacing: {\n      type: 'boolean',\n      description: 'remove spacing between features',\n      defaultValue: false,\n    },\n    largeInsertionIndicatorScale: {\n      type: 'number',\n      description:\n        'scale at which to draw the large insertion indicators (bp/pixel)',\n      defaultValue: 10,\n    },\n    mismatchAlpha: {\n      type: 'boolean',\n      defaultValue: false,\n      description: 'Fade low quality mismatches',\n    },\n  },\n  { explicitlyTyped: true },\n)\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport PileupRenderer from './PileupRenderer'\nimport ReactComponent from './components/PileupRendering'\nimport configSchema from './configSchema'\n\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addRendererType(\n    () =>\n      new PileupRenderer({\n        name: 'PileupRenderer',\n        ReactComponent,\n        configSchema,\n        pluginManager,\n      }),\n  )\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nconst configModelFactory = (pluginManager: PluginManager) => {\n  const PileupDisplayConfigSchema = pluginManager.getDisplayType(\n    'LinearPileupDisplay',\n  ).configSchema\n  const SNPCoverageDisplayConfigSchema = pluginManager.getDisplayType(\n    'LinearSNPCoverageDisplay',\n  ).configSchema\n\n  return ConfigurationSchema(\n    'LinearAlignmentsDisplay',\n    {\n      pileupDisplay: PileupDisplayConfigSchema,\n      snpCoverageDisplay: SNPCoverageDisplayConfigSchema,\n    },\n    { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n  )\n}\n\nexport type AlignmentsConfigModel = ReturnType<typeof configModelFactory>\nexport default configModelFactory\n","import React from 'react'\nimport {\n  ConfigurationReference,\n  AnyConfigurationModel,\n  getConf,\n} from '@jbrowse/core/configuration'\nimport { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { MenuItem } from '@jbrowse/core/ui'\nimport { autorun, when } from 'mobx'\nimport { addDisposer, getSnapshot, Instance, types } from 'mobx-state-tree'\nimport { getContainingTrack } from '@jbrowse/core/util'\nimport deepEqual from 'fast-deep-equal'\nimport { AlignmentsConfigModel } from './configSchema'\n\nconst minDisplayHeight = 20\nconst stateModelFactory = (\n  pluginManager: PluginManager,\n  configSchema: AlignmentsConfigModel,\n) => {\n  return types\n    .compose(\n      'LinearAlignmentsDisplay',\n      BaseDisplay,\n      types.model({\n        PileupDisplay: types.maybe(\n          pluginManager.getDisplayType('LinearPileupDisplay').stateModel,\n        ),\n        SNPCoverageDisplay: types.maybe(\n          pluginManager.getDisplayType('LinearSNPCoverageDisplay').stateModel,\n        ),\n        snpCovHeight: 45,\n        type: types.literal('LinearAlignmentsDisplay'),\n        configuration: ConfigurationReference(configSchema),\n        height: 250,\n        showCoverage: true,\n        showPileup: true,\n        userFeatureScreenDensity: types.maybe(types.number),\n      }),\n    )\n    .volatile(() => ({\n      scrollTop: 0,\n    }))\n    .actions(self => ({\n      toggleCoverage() {\n        self.showCoverage = !self.showCoverage\n      },\n      togglePileup() {\n        self.showPileup = !self.showPileup\n      },\n      setScrollTop(scrollTop: number) {\n        self.scrollTop = scrollTop\n      },\n      setSNPCoverageHeight(n: number) {\n        self.snpCovHeight = n\n      },\n    }))\n    .views(self => {\n      const { trackMenuItems: superTrackMenuItems } = self\n      return {\n        get pileupDisplayConfig() {\n          const conf = getConf(self, 'pileupDisplay')\n          const track = getContainingTrack(self)\n          return {\n            ...conf,\n            type: 'LinearPileupDisplay',\n            name: `${getConf(track, 'name')} pileup`,\n            displayId: `${self.configuration.displayId}_pileup_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this\n          }\n        },\n\n        getFeatureByID(blockKey: string, id: string) {\n          return self.PileupDisplay.getFeatureByID(blockKey, id)\n        },\n        searchFeatureByID(id: string) {\n          return self.PileupDisplay.searchFeatureByID(id)\n        },\n\n        get features() {\n          return self.PileupDisplay.features\n        },\n\n        get DisplayBlurb() {\n          return self.PileupDisplay?.DisplayBlurb\n        },\n\n        get sortedBy() {\n          return self.PileupDisplay.sortedBy\n        },\n        get sortedByPosition() {\n          return self.PileupDisplay.sortedByPosition\n        },\n        get sortedByRefName() {\n          return self.PileupDisplay.sortedByRefName\n        },\n\n        get snpCoverageDisplayConfig() {\n          const conf = getConf(self, 'snpCoverageDisplay')\n          const track = getContainingTrack(self)\n          return {\n            ...conf,\n            type: 'LinearSNPCoverageDisplay',\n            name: `${getConf(track, 'name')} snp coverage`,\n            displayId: `${self.configuration.displayId}_snpcoverage_xyz`, // xyz to avoid someone accidentally naming the displayId similar to this\n          }\n        },\n\n        trackMenuItems(): MenuItem[] {\n          return [\n            ...superTrackMenuItems(),\n            {\n              type: 'subMenu',\n              label: 'Pileup settings',\n              subMenu: self.PileupDisplay.trackMenuItems(),\n            },\n            {\n              type: 'subMenu',\n              label: 'SNPCoverage settings',\n              subMenu: self.SNPCoverageDisplay.trackMenuItems(),\n            },\n          ]\n        },\n      }\n    })\n    .actions(self => ({\n      setSNPCoverageDisplay(displayConfig: AnyConfigurationModel) {\n        self.SNPCoverageDisplay = {\n          type: 'LinearSNPCoverageDisplay',\n          configuration: displayConfig,\n          height: self.snpCovHeight,\n        }\n      },\n      setUserFeatureScreenDensity(limit: number) {\n        self.PileupDisplay.setUserFeatureScreenDensity(limit)\n        self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit)\n      },\n      setPileupDisplay(displayConfig: AnyConfigurationModel) {\n        self.PileupDisplay = {\n          type: 'LinearPileupDisplay',\n          configuration: displayConfig,\n        }\n      },\n      setHeight(displayHeight: number) {\n        if (displayHeight > minDisplayHeight) {\n          self.height = displayHeight\n        } else {\n          self.height = minDisplayHeight\n        }\n        return self.height\n      },\n      resizeHeight(distance: number) {\n        const oldHeight = self.height\n        const newHeight = this.setHeight(self.height + distance)\n        return newHeight - oldHeight\n      },\n    }))\n    .actions(self => ({\n      afterAttach() {\n        addDisposer(\n          self,\n          autorun(() => {\n            if (!self.SNPCoverageDisplay) {\n              self.setSNPCoverageDisplay(self.snpCoverageDisplayConfig)\n            } else if (\n              !deepEqual(\n                self.snpCoverageDisplayConfig,\n                getSnapshot(self.SNPCoverageDisplay.configuration),\n              )\n            ) {\n              self.SNPCoverageDisplay.setHeight(self.snpCovHeight)\n              self.SNPCoverageDisplay.setConfig(self.snpCoverageDisplayConfig)\n            }\n\n            if (!self.PileupDisplay) {\n              self.setPileupDisplay(self.pileupDisplayConfig)\n            } else if (\n              !deepEqual(\n                self.pileupDisplayConfig,\n                getSnapshot(self.PileupDisplay.configuration),\n              )\n            ) {\n              self.PileupDisplay.setConfig(self.pileupDisplayConfig)\n            }\n\n            // propagate the filterBy setting from pileupdisplay to snpcoverage\n            // note: the snpcoverage display is not able to control filterBy\n            // itself\n            if (\n              self.PileupDisplay.filterBy &&\n              !deepEqual(\n                getSnapshot(self.PileupDisplay.filterBy),\n                getSnapshot(self.SNPCoverageDisplay.filterBy),\n              )\n            ) {\n              self.SNPCoverageDisplay.setFilterBy(\n                getSnapshot(self.PileupDisplay.filterBy),\n              )\n            }\n            if (\n              self.PileupDisplay.colorBy &&\n              !deepEqual(\n                getSnapshot(self.PileupDisplay.colorBy),\n                self.SNPCoverageDisplay.colorBy\n                  ? getSnapshot(self.SNPCoverageDisplay.colorBy)\n                  : {},\n              )\n            ) {\n              self.SNPCoverageDisplay.setColorBy(\n                getSnapshot(self.PileupDisplay.colorBy),\n              )\n            }\n          }),\n        )\n        addDisposer(\n          self,\n          autorun(() => {\n            self.setSNPCoverageHeight(self.SNPCoverageDisplay.height)\n          }),\n        )\n      },\n      async renderSvg(opts: { rasterizeLayers?: boolean }) {\n        const pileupHeight = self.height - self.SNPCoverageDisplay.height\n        await when(() => self.PileupDisplay.ready)\n        return (\n          <>\n            <g>{await self.SNPCoverageDisplay.renderSvg(opts)}</g>\n            <g transform={`translate(0 ${self.SNPCoverageDisplay.height})`}>\n              {await self.PileupDisplay.renderSvg({\n                ...opts,\n                overrideHeight: pileupHeight,\n              })}\n            </g>\n          </>\n        )\n      },\n    }))\n}\n\nexport default stateModelFactory\nexport type AlignmentsDisplayStateModel = ReturnType<typeof stateModelFactory>\nexport type AlignmentsDisplayModel = Instance<AlignmentsDisplayStateModel>\n","import React from 'react'\nimport { observer } from 'mobx-react'\nimport { getConf } from '@jbrowse/core/configuration'\nimport { ResizeHandle } from '@jbrowse/core/ui'\nimport { makeStyles } from '@material-ui/core'\nimport { AlignmentsDisplayModel } from '../models/model'\n\nconst useStyles = makeStyles(() => ({\n  resizeHandle: {\n    height: 2,\n    position: 'absolute',\n    zIndex: 2,\n  },\n}))\n\nfunction AlignmentsDisplay({ model }: { model: AlignmentsDisplayModel }) {\n  const { PileupDisplay, SNPCoverageDisplay, showPileup, showCoverage } = model\n  const classes = useStyles()\n  const top = SNPCoverageDisplay.height\n  return (\n    <div\n      data-testid={`display-${getConf(model, 'displayId')}`}\n      style={{ position: 'relative' }}\n    >\n      {showCoverage ? (\n        <>\n          <div data-testid=\"Blockset-snpcoverage\">\n            <SNPCoverageDisplay.RenderingComponent model={SNPCoverageDisplay} />\n          </div>\n          <ResizeHandle\n            onDrag={delta => {\n              SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta)\n              return delta\n            }}\n            className={classes.resizeHandle}\n            style={{\n              top,\n            }}\n          />\n        </>\n      ) : null}\n\n      {showPileup ? (\n        <div\n          data-testid=\"Blockset-pileup\"\n          style={{\n            position: 'absolute',\n            top: showCoverage ? SNPCoverageDisplay.height : 0,\n          }}\n        >\n          <PileupDisplay.RenderingComponent model={PileupDisplay} />\n        </div>\n      ) : null}\n    </div>\n  )\n}\n\nexport default observer(AlignmentsDisplay)\n","import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\nimport PluginManager from '@jbrowse/core/PluginManager'\n// locals\nimport configSchemaFactory from './models/configSchema'\nimport modelFactory from './models/model'\nimport ReactComponent from './components/AlignmentsDisplay'\n\nexport default function (pluginManager: PluginManager) {\n  pluginManager.addDisplayType(() => {\n    const configSchema = configSchemaFactory(pluginManager)\n    return new DisplayType({\n      name: 'LinearAlignmentsDisplay',\n      configSchema,\n      stateModel: modelFactory(pluginManager, configSchema),\n      trackType: 'AlignmentsTrack',\n      viewType: 'LinearGenomeView',\n      ReactComponent,\n    })\n  })\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'\nimport { types } from 'mobx-state-tree'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function SNPCoverageConfigFactory(pluginManager: PluginManager) {\n  const SNPCoverageRendererConfigSchema = pluginManager.getRendererType(\n    'SNPCoverageRenderer',\n  ).configSchema\n\n  return ConfigurationSchema(\n    'LinearSNPCoverageDisplay',\n    {\n      autoscale: {\n        type: 'stringEnum',\n        defaultValue: 'local',\n        model: types.enumeration('Autoscale type', ['local']),\n        description:\n          'performs local autoscaling (no other options for SNP Coverage available)',\n      },\n      minScore: {\n        type: 'number',\n        defaultValue: Number.MIN_VALUE,\n        description: 'minimum value for the y-scale',\n      },\n      maxScore: {\n        type: 'number',\n        description: 'maximum value for the y-scale',\n        defaultValue: Number.MAX_VALUE,\n      },\n      scaleType: {\n        type: 'stringEnum',\n        model: types.enumeration('Scale type', ['linear', 'log']), // todo zscale\n        description: 'The type of scale to use',\n        defaultValue: 'linear',\n      },\n      inverted: {\n        type: 'boolean',\n        description: 'draw upside down',\n        defaultValue: false,\n      },\n\n      multiTicks: {\n        type: 'boolean',\n        description: 'Display multiple values for the ticks',\n        defaultValue: false,\n      },\n\n      renderers: ConfigurationSchema('RenderersConfiguration', {\n        SNPCoverageRenderer: SNPCoverageRendererConfigSchema,\n      }),\n    },\n    { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },\n  )\n}\n","/* eslint-disable @typescript-eslint/no-explicit-any */\nimport React from 'react'\nimport { observer } from 'mobx-react'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { Tooltip } from '@jbrowse/plugin-wiggle'\n\ntype Count = {\n  [key: string]: {\n    total: number\n    strands: { [key: string]: number }\n  }\n}\n\ntype SNPInfo = {\n  ref: Count\n  cov: Count\n  lowqual: Count\n  noncov: Count\n  delskips: Count\n  total: number\n}\n\nconst en = (n: number) => n.toLocaleString('en-US')\n\nconst TooltipContents = React.forwardRef(\n  ({ feature }: { feature: Feature }, ref: any) => {\n    const start = feature.get('start')\n    const end = feature.get('end')\n    const name = feature.get('refName')\n    const info = feature.get('snpinfo') as SNPInfo\n    const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]\n      .filter(f => !!f)\n      .join(':')\n\n    const total = info?.total\n\n    return (\n      <div ref={ref}>\n        <table>\n          <caption>{loc}</caption>\n          <thead>\n            <tr>\n              <th>Base</th>\n              <th>Count</th>\n              <th>% of Total</th>\n              <th>Strands</th>\n              <th>Source</th>\n            </tr>\n          </thead>\n          <tbody>\n            <tr>\n              <td>Total</td>\n              <td>{total}</td>\n              <td />\n            </tr>\n\n            {Object.entries(info).map(([key, entry]) => {\n              return Object.entries(entry).map(([base, score]) => {\n                const { strands } = score\n                return (\n                  <tr key={base}>\n                    <td>{base.toUpperCase()}</td>\n                    <td>{score.total}</td>\n                    <td>\n                      {base === 'total' || base === 'skip'\n                        ? '---'\n                        : `${Math.floor(\n                            (score.total / (total || score.total || 1)) * 100,\n                          )}%`}\n                    </td>\n                    <td>\n                      {strands['-1'] ? `${strands['-1']}(-)` : ''}\n                      {strands['1'] ? `${strands['1']}(+)` : ''}\n                    </td>\n                    <td>{key}</td>\n                  </tr>\n                )\n              })\n            })}\n          </tbody>\n        </table>\n      </div>\n    )\n  },\n)\n\ntype Coord = [number, number]\n\nconst SNPCoverageTooltip = observer(\n  (props: {\n    model: any\n    height: number\n    offsetMouseCoord: Coord\n    clientMouseCoord: Coord\n    clientRect?: DOMRect\n  }) => {\n    const { model } = props\n    const { featureUnderMouse: feat } = model\n    return feat && feat.get('type') === 'skip' ? null : (\n      <Tooltip TooltipContents={TooltipContents} {...props} />\n    )\n  },\n)\n\nexport default SNPCoverageTooltip\n","import { BlockSet } from '@jbrowse/core/util/blockTypes'\n\nimport { getSession } from '@jbrowse/core/util'\nimport { getRpcSessionId } from '@jbrowse/core/util/tracks'\nimport { IAnyStateTreeNode } from 'mobx-state-tree'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'\n\nexport async function getUniqueTagValues(\n  self: IAnyStateTreeNode & { adapterConfig: AnyConfigurationModel },\n  colorScheme: { type: string; tag?: string },\n  blocks: BlockSet,\n  opts?: {\n    headers?: Record<string, string>\n    signal?: AbortSignal\n    filters?: string[]\n  },\n) {\n  const { rpcManager } = getSession(self)\n  const { adapterConfig } = self\n  const sessionId = getRpcSessionId(self)\n  const values = await rpcManager.call(\n    getRpcSessionId(self),\n    'PileupGetGlobalValueForTag',\n    {\n      adapterConfig,\n      tag: colorScheme.tag,\n      sessionId,\n      regions: blocks.contentBlocks,\n      ...opts,\n    },\n  )\n  return values as string[]\n}\n\nexport async function getUniqueModificationValues(\n  self: IAnyStateTreeNode & {\n    parentTrack: IAnyStateTreeNode & { configuration: AnyConfigurationModel }\n  },\n  adapterConfig: AnyConfigurationModel,\n  colorScheme: { type: string; tag?: string },\n  blocks: BlockSet,\n  opts?: {\n    headers?: Record<string, string>\n    signal?: AbortSignal\n    filters?: string[]\n  },\n) {\n  const { rpcManager } = getSession(self)\n  const sessionId = getRpcSessionId(self)\n  const values = await rpcManager.call(\n    sessionId,\n    'PileupGetVisibleModifications',\n    {\n      adapterConfig,\n      tag: colorScheme.tag,\n      sessionId,\n      regions: blocks.contentBlocks,\n      ...opts,\n    },\n  )\n  return values as string[]\n}\n","import { addDisposer, types, cast, getEnv, getSnapshot } from 'mobx-state-tree'\nimport { observable, autorun } from 'mobx'\nimport { getConf, readConfObject } from '@jbrowse/core/configuration'\nimport { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle'\nimport {\n  AnyConfigurationSchemaType,\n  AnyConfigurationModel,\n} from '@jbrowse/core/configuration/configurationSchema'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'\nimport { getContainingView } from '@jbrowse/core/util'\nimport Tooltip from '../components/Tooltip'\nimport { getUniqueModificationValues } from '../../shared'\nimport { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\n// using a map because it preserves order\nconst rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']])\n\ntype LGV = LinearGenomeViewModel\n\nconst stateModelFactory = (\n  pluginManager: PluginManager,\n  configSchema: AnyConfigurationSchemaType,\n) =>\n  types\n    .compose(\n      'LinearSNPCoverageDisplay',\n      linearWiggleDisplayModelFactory(pluginManager, configSchema),\n      types.model({\n        type: types.literal('LinearSNPCoverageDisplay'),\n        drawInterbaseCounts: types.maybe(types.boolean),\n        drawIndicators: types.maybe(types.boolean),\n        drawArcs: types.maybe(types.boolean),\n        filterBy: types.optional(\n          types.model({\n            flagInclude: types.optional(types.number, 0),\n            flagExclude: types.optional(types.number, 1540),\n            readName: types.maybe(types.string),\n            tagFilter: types.maybe(\n              types.model({ tag: types.string, value: types.string }),\n            ),\n          }),\n          {},\n        ),\n        colorBy: types.maybe(\n          types.model({\n            type: types.string,\n            tag: types.maybe(types.string),\n          }),\n        ),\n      }),\n    )\n    .volatile(() => ({\n      modificationTagMap: observable.map({}),\n    }))\n    .actions(self => ({\n      setConfig(configuration: AnyConfigurationModel) {\n        self.configuration = configuration\n      },\n      setFilterBy(filter: {\n        flagInclude: number\n        flagExclude: number\n        readName?: string\n        tagFilter?: { tag: string; value: string }\n      }) {\n        self.filterBy = cast(filter)\n      },\n      setColorBy(colorBy?: { type: string; tag?: string }) {\n        self.colorBy = cast(colorBy)\n      },\n\n      updateModificationColorMap(uniqueModifications: string[]) {\n        const colorPalette = ['red', 'blue', 'green', 'orange', 'purple']\n        let i = 0\n\n        uniqueModifications.forEach(value => {\n          if (!self.modificationTagMap.has(value)) {\n            const newColor = colorPalette[i++]\n            self.modificationTagMap.set(value, newColor)\n          }\n        })\n      },\n    }))\n    .views(self => {\n      const { renderProps: superRenderProps } = self\n      return {\n        get rendererConfig() {\n          const configBlob =\n            getConf(self, ['renderers', self.rendererTypeName]) || {}\n\n          return self.rendererType.configSchema.create(\n            {\n              ...configBlob,\n              drawInterbaseCounts:\n                self.drawInterbaseCounts === undefined\n                  ? configBlob.drawInterbaseCounts\n                  : self.drawInterbaseCounts,\n              drawIndicators:\n                self.drawIndicators === undefined\n                  ? configBlob.drawIndicators\n                  : self.drawIndicators,\n              drawArcs:\n                self.drawArcs === undefined\n                  ? configBlob.drawArcs\n                  : self.drawArcs,\n            },\n            getEnv(self),\n          )\n        },\n        get drawArcsSetting() {\n          return self.drawArcs !== undefined\n            ? self.drawArcs\n            : readConfObject(this.rendererConfig, 'drawArcs')\n        },\n        get drawInterbaseCountsSetting() {\n          return self.drawInterbaseCounts !== undefined\n            ? self.drawInterbaseCounts\n            : readConfObject(this.rendererConfig, 'drawInterbaseCounts')\n        },\n        get drawIndicatorsSetting() {\n          return self.drawIndicators !== undefined\n            ? self.drawIndicators\n            : readConfObject(this.rendererConfig, 'drawIndicators')\n        },\n\n        get modificationsReady() {\n          return self.colorBy?.type === 'modifications'\n            ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap)))\n                .length > 0\n            : true\n        },\n\n        renderProps() {\n          const superProps = superRenderProps()\n          return {\n            ...superProps,\n            notReady: superProps.notReady || !this.modificationsReady,\n            filters: self.filters,\n            modificationTagMap: JSON.parse(\n              JSON.stringify(self.modificationTagMap),\n            ),\n\n            // must use getSnapshot because otherwise changes to e.g. just the\n            // colorBy.type are not read\n            colorBy: self.colorBy ? getSnapshot(self.colorBy) : undefined,\n          }\n        },\n      }\n    })\n    .actions(self => ({\n      toggleDrawIndicators() {\n        self.drawIndicators = !self.drawIndicatorsSetting\n      },\n      toggleDrawInterbaseCounts() {\n        self.drawInterbaseCounts = !self.drawInterbaseCountsSetting\n      },\n      toggleDrawArcs() {\n        self.drawArcs = !self.drawArcsSetting\n      },\n      afterAttach() {\n        addDisposer(\n          self,\n          autorun(\n            async () => {\n              try {\n                const { colorBy } = self\n                const { staticBlocks } = getContainingView(self) as LGV\n                if (colorBy?.type === 'modifications') {\n                  const vals = await getUniqueModificationValues(\n                    self,\n                    getConf(self.parentTrack, 'adapter'),\n                    colorBy,\n                    staticBlocks,\n                  )\n                  self.updateModificationColorMap(vals)\n                }\n              } catch (error) {\n                console.error(error)\n                self.setError(error)\n              }\n            },\n            { delay: 1000 },\n          ),\n        )\n      },\n    }))\n\n    .views(self => {\n      const { trackMenuItems: superTrackMenuItems } = self\n      return {\n        get TooltipComponent() {\n          return Tooltip\n        },\n\n        get adapterConfig() {\n          const subadapter = getConf(self.parentTrack, 'adapter')\n          return {\n            type: 'SNPCoverageAdapter',\n            subadapter,\n          }\n        },\n\n        get rendererTypeName() {\n          return rendererTypes.get('snpcoverage')\n        },\n\n        get needsScalebar() {\n          return true\n        },\n\n        contextMenuItems() {\n          return []\n        },\n\n        trackMenuItems() {\n          return [\n            ...superTrackMenuItems(),\n            {\n              label: 'Draw insertion/clipping indicators',\n              type: 'checkbox',\n              checked: self.drawIndicatorsSetting,\n              onClick: () => {\n                self.toggleDrawIndicators()\n              },\n            },\n            {\n              label: 'Draw insertion/clipping counts',\n              type: 'checkbox',\n              checked: self.drawInterbaseCountsSetting,\n              onClick: () => {\n                self.toggleDrawInterbaseCounts()\n              },\n            },\n            {\n              label: 'Draw arcs',\n              type: 'checkbox',\n              checked: self.drawArcsSetting,\n              onClick: () => {\n                self.toggleDrawArcs()\n              },\n            },\n          ]\n        },\n        // The SNPCoverage filters are called twice because the BAM/CRAM\n        // features pass filters and then the SNPCoverage score features pass\n        // through here, and are already have 'snpinfo' are passed through\n        get filters() {\n          let filters: string[] = []\n          if (self.filterBy) {\n            const { flagInclude, flagExclude, tagFilter, readName } =\n              self.filterBy\n            filters = [\n              `jexl:get(feature,'snpinfo') != undefined ? true : ` +\n                `((get(feature,'flags')&${flagInclude})==${flagInclude}) && ` +\n                `!((get(feature,'flags')&${flagExclude}))`,\n            ]\n\n            if (tagFilter) {\n              const { tag, value } = tagFilter\n              filters.push(\n                `jexl:get(feature,'snpinfo') != undefined ? true : ` +\n                  `\"${value}\" =='*' ? getTag(feature,\"${tag}\") != undefined : ` +\n                  `getTag(feature,\"${tag}\") == \"${value}\"`,\n              )\n            }\n            if (readName) {\n              filters.push(\n                `jexl:get(feature,'snpinfo') != undefined ? true : ` +\n                  `get(feature,'name') == \"${readName}\"`,\n              )\n            }\n          }\n          return new SerializableFilterChain({ filters })\n        },\n      }\n    })\n\nexport type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>\n\nexport default stateModelFactory\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport configSchemaFactory from './models/configSchema'\nimport modelFactory from './models/model'\nimport { LinearWiggleDisplayReactComponent } from '@jbrowse/plugin-wiggle'\nimport DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\n\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addDisplayType(() => {\n    const configSchema = configSchemaFactory(pluginManager)\n    return new DisplayType({\n      name: 'LinearSNPCoverageDisplay',\n      configSchema,\n      stateModel: modelFactory(pluginManager, configSchema),\n      trackType: 'AlignmentsTrack',\n      viewType: 'LinearGenomeView',\n      ReactComponent: LinearWiggleDisplayReactComponent,\n    })\n  })\n}\n","import { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { linearBasicDisplayConfigSchemaFactory } from '@jbrowse/plugin-linear-genome-view'\nimport { types, Instance } from 'mobx-state-tree'\nimport PluginManager from '@jbrowse/core/PluginManager'\n\nfunction PileupConfigFactory(pluginManager: PluginManager) {\n  const PileupRendererConfigSchema =\n    pluginManager.getRendererType('PileupRenderer').configSchema\n  const SvgFeatureRendererConfigSchema =\n    pluginManager.getRendererType('SvgFeatureRenderer').configSchema\n\n  // modify config schema to take in a sub coverage display\n  return ConfigurationSchema(\n    'LinearPileupDisplay',\n    {\n      defaultRendering: {\n        type: 'stringEnum',\n        model: types.enumeration('Rendering', ['pileup', 'svg']),\n        defaultValue: 'pileup',\n      },\n      renderers: ConfigurationSchema('RenderersConfiguration', {\n        PileupRenderer: PileupRendererConfigSchema,\n        SvgFeatureRenderer: SvgFeatureRendererConfigSchema,\n      }),\n      renderer: '',\n      maxFeatureScreenDensity: {\n        type: 'number',\n        description: 'maximum features per pixel that is displayed in the view',\n        defaultValue: 5,\n      },\n      colorScheme: {\n        type: 'stringEnum',\n        model: types.enumeration('colorScheme', [\n          'strand',\n          'normal',\n          'insertSize',\n          'insertSizeAndOrientation',\n          'mappingQuality',\n          'tag',\n        ]),\n        description: 'color scheme to use',\n        defaultValue: 'normal',\n      },\n    },\n    {\n      baseConfiguration: linearBasicDisplayConfigSchemaFactory(pluginManager),\n      explicitlyTyped: true,\n    },\n  )\n}\n\nexport type LinearPileupDisplayConfigModel = ReturnType<\n  typeof PileupConfigFactory\n>\nexport type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>\nexport default PileupConfigFactory\n","import React from 'react'\nimport { observer } from 'mobx-react'\nimport Typography from '@material-ui/core/Typography'\n\nexport interface LinearPileupDisplayBlurbProps {\n  model: {\n    sortedBy?: {\n      pos: number\n      refName: number\n      type: string\n    }\n  }\n}\n\nfunction LinearPileupDisplayBlurb(props: LinearPileupDisplayBlurbProps) {\n  const { model } = props\n  const { sortedBy } = model\n  return sortedBy ? (\n    <div\n      data-testid={`blurb-${model.sortedBy}`}\n      style={{ backgroundColor: 'white' }}\n    >\n      <Typography color=\"secondary\" variant=\"caption\">\n        {model.sortedBy\n          ? `Sorted by ${sortedBy.type.toLowerCase()} at ${sortedBy.refName}:${\n              sortedBy.pos\n            }`\n          : null}\n      </Typography>\n    </div>\n  ) : null\n}\nexport default observer(LinearPileupDisplayBlurb)\n","import { lazy } from 'react'\nimport {\n  ConfigurationReference,\n  readConfObject,\n  getConf,\n} from '@jbrowse/core/configuration'\nimport { getRpcSessionId } from '@jbrowse/core/util/tracks'\nimport {\n  getSession,\n  isSessionModelWithWidgets,\n  getContainingView,\n} from '@jbrowse/core/util'\n\nimport VisibilityIcon from '@material-ui/icons/Visibility'\nimport { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons'\nimport {\n  LinearGenomeViewModel,\n  BaseLinearDisplay,\n} from '@jbrowse/plugin-linear-genome-view'\nimport { cast, types, addDisposer, getEnv, Instance } from 'mobx-state-tree'\nimport copy from 'copy-to-clipboard'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport MenuOpenIcon from '@material-ui/icons/MenuOpen'\nimport SortIcon from '@material-ui/icons/Sort'\nimport PaletteIcon from '@material-ui/icons/Palette'\nimport FilterListIcon from '@material-ui/icons/ClearAll'\n\nimport { autorun, observable } from 'mobx'\nimport { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'\nimport SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'\nimport { LinearPileupDisplayConfigModel } from './configSchema'\nimport LinearPileupDisplayBlurb from './components/LinearPileupDisplayBlurb'\n\nimport { getUniqueTagValues, getUniqueModificationValues } from '../shared'\n\nconst ColorByTagDlg = lazy(() => import('./components/ColorByTag'))\nconst FilterByTagDlg = lazy(() => import('./components/FilterByTag'))\nconst SortByTagDlg = lazy(() => import('./components/SortByTag'))\nconst SetFeatureHeightDlg = lazy(() => import('./components/SetFeatureHeight'))\nconst SetMaxHeightDlg = lazy(() => import('./components/SetMaxHeight'))\nconst ModificationsDlg = lazy(() => import('./components/ColorByModifications'))\n\n// using a map because it preserves order\nconst rendererTypes = new Map([\n  ['pileup', 'PileupRenderer'],\n  ['svg', 'SvgFeatureRenderer'],\n])\n\ntype LGV = LinearGenomeViewModel\n\nconst stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>\n  types\n    .compose(\n      'LinearPileupDisplay',\n      BaseLinearDisplay,\n      types.model({\n        type: types.literal('LinearPileupDisplay'),\n        configuration: ConfigurationReference(configSchema),\n        showSoftClipping: false,\n        featureHeight: types.maybe(types.number),\n        noSpacing: types.maybe(types.boolean),\n        fadeLikelihood: types.maybe(types.boolean),\n        trackMaxHeight: types.maybe(types.number),\n        mismatchAlpha: types.maybe(types.boolean),\n        sortedBy: types.maybe(\n          types.model({\n            type: types.string,\n            pos: types.number,\n            tag: types.maybe(types.string),\n            refName: types.string,\n            assemblyName: types.string,\n          }),\n        ),\n        colorBy: types.maybe(\n          types.model({\n            type: types.string,\n            tag: types.maybe(types.string),\n            extra: types.frozen(),\n          }),\n        ),\n        filterBy: types.optional(\n          types.model({\n            flagInclude: types.optional(types.number, 0),\n            flagExclude: types.optional(types.number, 1540),\n            readName: types.maybe(types.string),\n            tagFilter: types.maybe(\n              types.model({ tag: types.string, value: types.string }),\n            ),\n          }),\n          {},\n        ),\n      }),\n    )\n    .volatile(() => ({\n      colorTagMap: observable.map<string, string>({}),\n      modificationTagMap: observable.map<string, string>({}),\n      ready: false,\n    }))\n    .actions(self => ({\n      setReady(flag: boolean) {\n        self.ready = flag\n      },\n      setMaxHeight(n: number) {\n        self.trackMaxHeight = n\n      },\n      setFeatureHeight(n: number) {\n        self.featureHeight = n\n      },\n      setNoSpacing(flag: boolean) {\n        self.noSpacing = flag\n      },\n\n      setColorScheme(colorScheme: { type: string; tag?: string }) {\n        self.colorTagMap = observable.map({}) // clear existing mapping\n        self.colorBy = cast(colorScheme)\n        self.ready = false\n      },\n\n      updateModificationColorMap(uniqueModifications: string[]) {\n        const colorPalette = ['red', 'blue', 'green', 'orange', 'purple']\n        uniqueModifications.forEach(value => {\n          if (!self.modificationTagMap.has(value)) {\n            const totalKeys = [...self.modificationTagMap.keys()].length\n            const newColor = colorPalette[totalKeys]\n            self.modificationTagMap.set(value, newColor)\n          }\n        })\n      },\n\n      updateColorTagMap(uniqueTag: string[]) {\n        // pale color scheme https://cran.r-project.org/web/packages/khroma/vignettes/tol.html e.g. \"tol_light\"\n        const colorPalette = [\n          '#BBCCEE',\n          'pink',\n          '#CCDDAA',\n          '#EEEEBB',\n          '#FFCCCC',\n          'lightblue',\n          'lightgreen',\n          'tan',\n          '#CCEEFF',\n          'lightsalmon',\n        ]\n\n        uniqueTag.forEach(value => {\n          if (!self.colorTagMap.has(value)) {\n            const totalKeys = [...self.colorTagMap.keys()].length\n            const newColor = colorPalette[totalKeys]\n            self.colorTagMap.set(value, newColor)\n          }\n        })\n      },\n    }))\n    .actions(self => ({\n      afterAttach() {\n        addDisposer(\n          self,\n          autorun(\n            async () => {\n              try {\n                const { rpcManager } = getSession(self)\n                const { sortedBy, colorBy } = self\n                const view = getContainingView(self) as LGV\n\n                // continually generate the vc pairing, set and rerender if any\n                // new values seen\n                if (colorBy?.tag) {\n                  const uniqueTagSet = await getUniqueTagValues(\n                    self,\n                    colorBy,\n                    view.staticBlocks,\n                  )\n                  self.updateColorTagMap(uniqueTagSet)\n                }\n\n                if (colorBy?.type === 'modifications') {\n                  const uniqueModificationsSet =\n                    await getUniqueModificationValues(\n                      self,\n                      getConf(self.parentTrack, ['adapter']),\n                      colorBy,\n                      view.staticBlocks,\n                    )\n                  self.updateModificationColorMap(uniqueModificationsSet)\n                }\n\n                if (sortedBy) {\n                  const { pos, refName, assemblyName } = sortedBy\n\n                  const region = {\n                    start: pos,\n                    end: pos + 1,\n                    refName,\n                    assemblyName,\n                  }\n\n                  // render just the sorted region first\n                  await self.rendererType.renderInClient(rpcManager, {\n                    assemblyName,\n                    regions: [region],\n                    adapterConfig: self.adapterConfig,\n                    rendererType: self.rendererType.name,\n                    sessionId: getRpcSessionId(self),\n                    timeout: 1000000,\n                    ...self.renderProps(),\n                  })\n                  self.setReady(true)\n                  self.setCurrBpPerPx(view.bpPerPx)\n                } else {\n                  self.setReady(true)\n                }\n              } catch (e) {\n                console.error(e)\n                self.setError(e)\n              }\n            },\n            { delay: 1000 },\n          ),\n        )\n      },\n      selectFeature(feature: Feature) {\n        const session = getSession(self)\n        if (isSessionModelWithWidgets(session)) {\n          const featureWidget = session.addWidget(\n            'AlignmentsFeatureWidget',\n            'alignmentFeature',\n            { featureData: feature.toJSON(), view: getContainingView(self) },\n          )\n          session.showWidget(featureWidget)\n        }\n        session.setSelection(feature)\n      },\n\n      clearSelected() {\n        self.sortedBy = undefined\n      },\n\n      // uses copy-to-clipboard and generates notification\n      copyFeatureToClipboard(feature: Feature) {\n        const { uniqueId, ...rest } = feature.toJSON()\n        const session = getSession(self)\n        copy(JSON.stringify(rest, null, 4))\n        session.notify('Copied to clipboard', 'success')\n      },\n\n      toggleSoftClipping() {\n        self.showSoftClipping = !self.showSoftClipping\n      },\n      toggleMismatchAlpha() {\n        self.mismatchAlpha = !self.mismatchAlpha\n      },\n\n      setConfig(configuration: AnyConfigurationModel) {\n        self.configuration = configuration\n      },\n\n      setSortedBy(type: string, tag?: string) {\n        const { centerLineInfo } = getContainingView(self) as LGV\n        if (!centerLineInfo) {\n          return\n        }\n        const { refName, assemblyName, offset } = centerLineInfo\n        const centerBp = Math.round(offset) + 1\n        const centerRefName = refName\n\n        if (centerBp < 0) {\n          return\n        }\n\n        self.sortedBy = {\n          type,\n          pos: centerBp,\n          refName: centerRefName,\n          assemblyName,\n          tag,\n        }\n        self.ready = false\n      },\n      setFilterBy(filter: {\n        flagInclude: number\n        flagExclude: number\n        readName?: string\n        tagFilter?: { tag: string; value: string }\n      }) {\n        self.filterBy = cast(filter)\n      },\n    }))\n    .actions(self => {\n      // resets the sort object and refresh whole display on reload\n      const superReload = self.reload\n\n      return {\n        reload() {\n          self.clearSelected()\n          superReload()\n        },\n      }\n    })\n\n    .views(self => ({\n      get maxHeight() {\n        const conf = getConf(self, ['renderers', self.rendererTypeName]) || {}\n        return self.trackMaxHeight !== undefined\n          ? self.trackMaxHeight\n          : conf.maxHeight\n      },\n      get rendererConfig() {\n        const configBlob =\n          getConf(self, ['renderers', self.rendererTypeName]) || {}\n        return self.rendererType.configSchema.create(\n          {\n            ...configBlob,\n            height: self.featureHeight,\n            noSpacing: self.noSpacing,\n            maxHeight: this.maxHeight,\n            mismatchAlpha: self.mismatchAlpha,\n          },\n          getEnv(self),\n        )\n      },\n      get featureHeightSetting() {\n        return (\n          self.featureHeight || readConfObject(this.rendererConfig, 'height')\n        )\n      },\n      get mismatchAlphaSetting() {\n        return self.mismatchAlpha !== undefined\n          ? self.mismatchAlpha\n          : readConfObject(this.rendererConfig, 'mismatchAlpha')\n      },\n    }))\n    .views(self => {\n      const {\n        trackMenuItems: superTrackMenuItems,\n        renderProps: superRenderProps,\n      } = self\n\n      return {\n        get rendererTypeName() {\n          const viewName = getConf(self, 'defaultRendering')\n          const rendererType = rendererTypes.get(viewName)\n          if (!rendererType) {\n            throw new Error(`unknown alignments view name ${viewName}`)\n          }\n          return rendererType\n        },\n\n        contextMenuItems() {\n          const feat = self.contextMenuFeature\n          const contextMenuItems = feat\n            ? [\n                {\n                  label: 'Open feature details',\n                  icon: MenuOpenIcon,\n                  onClick: () => {\n                    self.clearFeatureSelection()\n                    if (feat) {\n                      self.selectFeature(feat)\n                    }\n                  },\n                },\n                {\n                  label: 'Copy info to clipboard',\n                  icon: ContentCopyIcon,\n                  onClick: () => {\n                    if (feat) {\n                      self.copyFeatureToClipboard(feat)\n                    }\n                  },\n                },\n              ]\n            : []\n          return contextMenuItems\n        },\n\n        get DisplayBlurb() {\n          return LinearPileupDisplayBlurb\n        },\n\n        get filters() {\n          let filters: string[] = []\n          const { flagInclude, flagExclude, tagFilter, readName } =\n            self.filterBy\n\n          filters = [\n            `jexl:((get(feature,'flags')&${flagInclude})==${flagInclude}) && !(get(feature,'flags')&${flagExclude})`,\n          ]\n          if (tagFilter) {\n            const { tag, value } = tagFilter\n            filters.push(\n              `jexl:\"${value}\" =='*' ? getTag(feature,\"${tag}\") != undefined : getTag(feature,\"${tag}\") == \"${value}\"`,\n            )\n          }\n          if (readName) {\n            filters.push(`jexl:get(feature,'name') == \"${readName}\"`)\n          }\n          return new SerializableFilterChain({ filters })\n        },\n\n        renderProps() {\n          const view = getContainingView(self) as LGV\n          const {\n            colorTagMap,\n            modificationTagMap,\n            sortedBy,\n            colorBy,\n            rpcDriverName,\n          } = self\n\n          const superProps = superRenderProps()\n\n          return {\n            ...superProps,\n            notReady:\n              superProps.notReady ||\n              !self.ready ||\n              (sortedBy && self.currBpPerPx !== view.bpPerPx),\n            rpcDriverName,\n            displayModel: self,\n            sortedBy,\n            colorBy,\n            colorTagMap: JSON.parse(JSON.stringify(colorTagMap)),\n            modificationTagMap: JSON.parse(JSON.stringify(modificationTagMap)),\n            filters: this.filters,\n            showSoftClip: self.showSoftClipping,\n            config: self.rendererConfig,\n          }\n        },\n\n        trackMenuItems() {\n          return [\n            ...superTrackMenuItems(),\n            {\n              label: 'Show soft clipping',\n              icon: VisibilityIcon,\n              type: 'checkbox',\n              checked: self.showSoftClipping,\n              onClick: () => {\n                self.toggleSoftClipping()\n                // if toggling from off to on, will break sort for this track\n                // so clear it\n                if (self.showSoftClipping) {\n                  self.clearSelected()\n                }\n              },\n            },\n            {\n              label: 'Sort by',\n              icon: SortIcon,\n              disabled: self.showSoftClipping,\n              subMenu: [\n                ...['Start location', 'Read strand', 'Base pair'].map(\n                  option => {\n                    return {\n                      label: option,\n                      onClick: () => self.setSortedBy(option),\n                    }\n                  },\n                ),\n                {\n                  label: 'Sort by tag...',\n                  onClick: () => {\n                    getSession(self).queueDialog(doneCallback => [\n                      SortByTagDlg,\n                      { model: self, handleClose: doneCallback },\n                    ])\n                  },\n                },\n                {\n                  label: 'Clear sort',\n                  onClick: () => self.clearSelected(),\n                },\n              ],\n            },\n            {\n              label: 'Color scheme',\n              icon: PaletteIcon,\n              subMenu: [\n                {\n                  label: 'Normal',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'normal' })\n                  },\n                },\n                {\n                  label: 'Mapping quality',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'mappingQuality' })\n                  },\n                },\n                {\n                  label: 'Strand',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'strand' })\n                  },\n                },\n                {\n                  label: 'Pair orientation',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'pairOrientation' })\n                  },\n                },\n                {\n                  label: 'Per-base quality',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'perBaseQuality' })\n                  },\n                },\n                {\n                  label: 'Modifications or methylation',\n                  onClick: () => {\n                    getSession(self).queueDialog(doneCallback => [\n                      ModificationsDlg,\n                      { model: self, handleClose: doneCallback },\n                    ])\n                  },\n                },\n                {\n                  label: 'Insert size',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'insertSize' })\n                  },\n                },\n                {\n                  label: 'Stranded paired-end',\n                  onClick: () => {\n                    self.setColorScheme({ type: 'reverseTemplate' })\n                  },\n                },\n                {\n                  label: 'Color by tag...',\n                  onClick: () => {\n                    getSession(self).queueDialog(doneCallback => [\n                      ColorByTagDlg,\n                      { model: self, handleClose: doneCallback },\n                    ])\n                  },\n                },\n              ],\n            },\n            {\n              label: 'Filter by',\n              icon: FilterListIcon,\n              onClick: () => {\n                getSession(self).queueDialog(doneCallback => [\n                  FilterByTagDlg,\n                  { model: self, handleClose: doneCallback },\n                ])\n              },\n            },\n            {\n              label: 'Set feature height',\n              onClick: () => {\n                getSession(self).queueDialog(doneCallback => [\n                  SetFeatureHeightDlg,\n                  { model: self, handleClose: doneCallback },\n                ])\n              },\n            },\n            {\n              label: 'Set max height',\n              onClick: () => {\n                getSession(self).queueDialog(doneCallback => [\n                  SetMaxHeightDlg,\n                  { model: self, handleClose: doneCallback },\n                ])\n              },\n            },\n            {\n              label: 'Fade mismatches by quality',\n              type: 'checkbox',\n              checked: self.mismatchAlphaSetting,\n              onClick: () => {\n                self.toggleMismatchAlpha()\n              },\n            },\n          ]\n        },\n      }\n    })\n\nexport type LinearPileupDisplayStateModel = ReturnType<typeof stateModelFactory>\nexport type LinearPileupDisplayModel = Instance<LinearPileupDisplayStateModel>\n\nexport default stateModelFactory\n","import configSchemaFactory from './configSchema'\nimport modelFactory from './model'\nimport DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view'\n\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addDisplayType(() => {\n    const configSchema = configSchemaFactory(pluginManager)\n    return new DisplayType({\n      name: 'LinearPileupDisplay',\n      configSchema,\n      stateModel: modelFactory(configSchema),\n      trackType: 'AlignmentsTrack',\n      viewType: 'LinearGenomeView',\n      ReactComponent: BaseLinearDisplayComponent,\n    })\n  })\n}\n","import PluginManager from '@jbrowse/core/PluginManager'\nimport TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport {\n  createBaseTrackConfig,\n  createBaseTrackModel,\n} from '@jbrowse/core/pluggableElementTypes/models'\nfunction configSchemaFactory(pluginManager: PluginManager) {\n  return ConfigurationSchema(\n    'AlignmentsTrack',\n    {},\n    { baseConfiguration: createBaseTrackConfig(pluginManager) },\n  )\n}\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addTrackType(() => {\n    const configSchema = configSchemaFactory(pluginManager)\n    const track = new TrackType({\n      name: 'AlignmentsTrack',\n      configSchema,\n      stateModel: createBaseTrackModel(\n        pluginManager,\n        'AlignmentsTrack',\n        configSchema,\n      ),\n    })\n    const linearAlignmentsDisplay = pluginManager.getDisplayType(\n      'LinearAlignmentsDisplay',\n    )\n    // Add LinearAlignmentsDisplay here so that it has priority over the other\n    // linear displays (defaults to order the displays are added, but we have\n    // to add the Pileup and SNPCoverage displays first).\n    track.addDisplayType(linearAlignmentsDisplay)\n    return track\n  })\n}\n","import { lazy } from 'react'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { ElementId } from '@jbrowse/core/util/types/mst'\nimport { types } from 'mobx-state-tree'\nimport WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'\n\nconst configSchema = ConfigurationSchema('AlignmentsFeatureWidget', {})\n\nexport function stateModelFactory(pluginManager: PluginManager) {\n  return types\n    .model('AlignmentsFeatureWidget', {\n      id: ElementId,\n      type: types.literal('AlignmentsFeatureWidget'),\n      featureData: types.frozen(),\n      view: types.safeReference(\n        pluginManager.pluggableMstType('view', 'stateModel'),\n      ),\n    })\n    .actions(self => ({\n      setFeatureData(data: unknown) {\n        self.featureData = data\n      },\n      clearFeatureData() {\n        self.featureData = undefined\n      },\n    }))\n}\n\nexport default function register(pluginManager: PluginManager) {\n  pluginManager.addWidgetType(\n    () =>\n      new WidgetType({\n        name: 'AlignmentsFeatureWidget',\n        heading: 'Feature details',\n        configSchema,\n        stateModel: stateModelFactory(pluginManager),\n        ReactComponent: lazy(() => import('./AlignmentsFeatureDetail')),\n      }),\n  )\n}\n\nexport { configSchema }\n","import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'\nimport { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'\nimport { renameRegionsIfNeeded } from '@jbrowse/core/util'\nimport { Region } from '@jbrowse/core/util/types'\nimport { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'\nimport { toArray } from 'rxjs/operators'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getTagAlt } from '../util'\nimport { getModificationTypes } from '../BamAdapter/MismatchParser'\n\nexport class PileupGetGlobalValueForTag extends RpcMethodType {\n  name = 'PileupGetGlobalValueForTag'\n\n  async serializeArguments(\n    args: RenderArgs & { signal?: AbortSignal; statusCallback?: Function },\n    rpcDriverClassName: string,\n  ) {\n    const { rootModel } = this.pluginManager\n    const assemblyManager = rootModel?.session?.assemblyManager\n    if (!assemblyManager) {\n      throw new Error('no assembly manager available')\n    }\n\n    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args)\n\n    return super.serializeArguments(renamedArgs, rpcDriverClassName)\n  }\n\n  async execute(\n    args: {\n      adapterConfig: {}\n      signal?: RemoteAbortSignal\n      headers?: Record<string, string>\n      regions: Region[]\n      sessionId: string\n      tag: string\n    },\n    rpcDriverClassName: string,\n  ) {\n    const deserializedArgs = await this.deserializeArguments(\n      args,\n      rpcDriverClassName,\n    )\n    const { adapterConfig, sessionId, regions, tag } = deserializedArgs\n    const dataAdapter = (\n      await getAdapter(this.pluginManager, sessionId, adapterConfig)\n    ).dataAdapter as BaseFeatureDataAdapter\n\n    const features = dataAdapter.getFeaturesInMultipleRegions(regions)\n    const featuresArray = await features.pipe(toArray()).toPromise()\n    const uniqueValues = new Set<string>()\n    featuresArray.forEach(feature => {\n      const tags = feature.get('tags')\n      const val = tags ? tags[tag] : feature.get(tag)\n      if (val !== undefined) {\n        uniqueValues.add(`${val}`)\n      }\n    })\n    return [...uniqueValues]\n  }\n}\n\nexport class PileupGetVisibleModifications extends RpcMethodType {\n  name = 'PileupGetVisibleModifications'\n\n  async serializeArguments(\n    args: RenderArgs & { signal?: AbortSignal; statusCallback?: Function },\n    rpcDriverClassName: string,\n  ) {\n    const { rootModel } = this.pluginManager\n    const assemblyManager = rootModel?.session?.assemblyManager\n    if (!assemblyManager) {\n      throw new Error('no assembly manager available')\n    }\n\n    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args)\n\n    return super.serializeArguments(renamedArgs, rpcDriverClassName)\n  }\n\n  async execute(\n    args: {\n      adapterConfig: {}\n      signal?: RemoteAbortSignal\n      headers?: Record<string, string>\n      regions: Region[]\n      sessionId: string\n      tag: string\n    },\n    rpcDriverClassName: string,\n  ) {\n    const deserializedArgs = await this.deserializeArguments(\n      args,\n      rpcDriverClassName,\n    )\n    const { adapterConfig, sessionId, regions } = deserializedArgs\n    const dataAdapter = (\n      await getAdapter(this.pluginManager, sessionId, adapterConfig)\n    ).dataAdapter as BaseFeatureDataAdapter\n\n    const features = dataAdapter.getFeaturesInMultipleRegions(regions)\n    const featuresArray = await features.pipe(toArray()).toPromise()\n    const uniqueValues = new Set<string>()\n    featuresArray.forEach(feature => {\n      const val = (getTagAlt(feature, 'MM', 'Mm') as string) || ''\n      if (val !== undefined) {\n        getModificationTypes(val).forEach(t => uniqueValues.add(t))\n      }\n    })\n    return [...uniqueValues]\n  }\n}\n","import { FileLocation } from '@jbrowse/core/util/types'\nimport Plugin from '@jbrowse/core/Plugin'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport * as MismatchParser from './BamAdapter/MismatchParser'\nimport { LinearPileupDisplayModel } from './LinearPileupDisplay/model'\n\nimport BamAdapterF from './CramAdapter'\nimport CramAdapterF from './BamAdapter'\nimport HtsgetBamAdapterF from './HtsgetBamAdapter'\nimport SNPCoverageAdapterF from './SNPCoverageAdapter'\nimport SNPCoverageRendererF from './SNPCoverageRenderer'\nimport PileupRendererF from './PileupRenderer'\nimport LinearAlignmentsDisplayF from './LinearAlignmentsDisplay'\nimport LinearSNPCoverageDisplayF from './LinearSNPCoverageDisplay'\nimport LinearPileupDisplayF from './LinearPileupDisplay'\nimport AlignmentsTrackF from './AlignmentsTrack'\nimport AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail'\n\nimport {\n  PileupGetGlobalValueForTag,\n  PileupGetVisibleModifications,\n} from './PileupRPC/rpcMethods'\nimport {\n  makeIndex,\n  makeIndexType,\n  getFileName,\n  AdapterGuesser,\n  TrackTypeGuesser,\n} from '@jbrowse/core/util/tracks'\n\nexport { MismatchParser }\nexport type { LinearPileupDisplayModel }\n\nexport default class AlignmentsPlugin extends Plugin {\n  name = 'AlignmentsPlugin'\n\n  install(pluginManager: PluginManager) {\n    ;[\n      CramAdapterF,\n      BamAdapterF,\n      LinearPileupDisplayF,\n      LinearSNPCoverageDisplayF,\n      AlignmentsTrackF,\n      SNPCoverageAdapterF,\n      HtsgetBamAdapterF,\n      PileupRendererF,\n      SNPCoverageRendererF,\n      LinearAlignmentsDisplayF,\n      AlignmentsFeatureWidgetF,\n    ].map(f => f(pluginManager))\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 = /\\.cram$/i\n          const adapterName = 'CramAdapter'\n          const fileName = getFileName(file)\n          const obj = {\n            type: adapterName,\n            cramLocation: file,\n            craiLocation: index || makeIndex(file, '.crai'),\n          }\n          if (regexGuess.test(fileName) && !adapterHint) {\n            return obj\n          } else if (adapterHint === adapterName) {\n            return obj\n          }\n          return adapterGuesser(file, index, adapterHint)\n        }\n      },\n    )\n\n    pluginManager.addToExtensionPoint(\n      'Core-guessAdapterForLocation',\n      (adapterGuesser: AdapterGuesser) => {\n        return (\n          file: FileLocation,\n          index?: FileLocation,\n          adapterHint?: string,\n        ) => {\n          const regexGuess = /\\.bam$/i\n          const adapterName = 'BamAdapter'\n          const fileName = getFileName(file)\n          const indexName = index && getFileName(index)\n\n          const obj = {\n            type: adapterName,\n            bamLocation: file,\n            index: {\n              location: index || makeIndex(file, '.bai'),\n              indexType: makeIndexType(indexName, 'CSI', 'BAI'),\n            },\n          }\n          if (regexGuess.test(fileName) && !adapterHint) {\n            return obj\n          } else if (adapterHint === adapterName) {\n            return obj\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 === 'BamAdapter' || adapterName === 'CramAdapter') {\n            return 'AlignmentsTrack'\n          }\n          return trackTypeGuesser(adapterName)\n        }\n      },\n    )\n\n    pluginManager.addRpcMethod(\n      () => new PileupGetGlobalValueForTag(pluginManager),\n    )\n    pluginManager.addRpcMethod(\n      () => new PileupGetVisibleModifications(pluginManager),\n    )\n  }\n}\n","/* eslint-disable no-underscore-dangle */\nimport {\n  Feature,\n  SimpleFeatureSerialized,\n} from '@jbrowse/core/util/simpleFeature'\n\nimport CramAdapter from './CramAdapter'\n\nexport interface Mismatch {\n  qual?: number\n  start: number\n  length: number\n  type: string\n  base: string\n  altbase?: string\n  seq?: string\n  cliplen?: number\n}\n\nexport default class CramSlightlyLazyFeature implements Feature {\n  private _store: CramAdapter\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  constructor(private record: any, store: CramAdapter) {\n    this._store = store\n  }\n\n  _get_name() {\n    return this.record.readName\n  }\n\n  _get_start() {\n    return this.record.alignmentStart - 1\n  }\n\n  _get_end() {\n    return this.record.alignmentStart + this.record.lengthOnRef - 1\n  }\n\n  _get_cram_read_features() {\n    return this.record.readFeatures\n  }\n\n  _get_type() {\n    return 'match'\n  }\n\n  _get_score() {\n    return this.record.mappingQuality\n  }\n\n  _get_flags() {\n    return this.record.flags\n  }\n\n  _get_strand() {\n    return this.record.isReverseComplemented() ? -1 : 1\n  }\n\n  _read_group_id() {\n    const rg = this._store.samHeader.readGroups\n    return rg ? rg[this.record.readGroupId] : undefined\n  }\n\n  _get_qual() {\n    return (this.record.qualityScores || []).join(' ')\n  }\n\n  qualRaw() {\n    return this.record.qualityScores\n  }\n\n  _get_seq_id() {\n    return this._store.refIdToName(this.record.sequenceId)\n  }\n\n  _get_refName() {\n    return this._get_seq_id()\n  }\n\n  _get_is_paired() {\n    return !!this.record.mate\n  }\n\n  _get_pair_orientation() {\n    return this.record.isPaired() ? this.record.getPairOrientation() : undefined\n  }\n\n  _get_template_length() {\n    return this.record.templateLength || this.record.templateSize\n  }\n\n  _get_next_seq_id() {\n    return this.record.mate\n      ? this._store.refIdToName(this.record.mate.sequenceId)\n      : undefined\n  }\n\n  _get_next_pos() {\n    return this.record.mate ? this.record.mate.alignmentStart : undefined\n  }\n\n  _get_next_segment_position() {\n    return this.record.mate\n      ? `${this._store.refIdToName(this.record.mate.sequenceId)}:${\n          this.record.mate.alignmentStart\n        }`\n      : undefined\n  }\n\n  _get_tags() {\n    const RG = this._read_group_id()\n    const { tags } = this.record\n    // avoids a tag copy if no RG, but just copy if there is one\n    return RG !== undefined ? { ...tags, RG } : tags\n  }\n\n  _get_seq() {\n    return this.record.getReadBases()\n  }\n\n  // generate a CIGAR, based on code from jkbonfield\n  _get_CIGAR() {\n    let seq = ''\n    let cigar = ''\n    let op = 'M'\n    let oplen = 0\n\n    // not sure I should access these, but...\n    const ref = this.record._refRegion.seq\n    const refStart = this.record._refRegion.start\n    let last_pos = this.record.alignmentStart\n    let sublen = 0\n    if (typeof this.record.readFeatures !== 'undefined') {\n      // @ts-ignore\n      this.record.readFeatures.forEach(({ code, refPos, sub, data }) => {\n        sublen = refPos - last_pos\n        seq += ref.substring(last_pos - refStart, refPos - refStart)\n        last_pos = refPos\n\n        if (oplen && op !== 'M') {\n          cigar += oplen + op\n          oplen = 0\n        }\n        if (sublen) {\n          op = 'M'\n          oplen += sublen\n        }\n\n        if (code === 'b') {\n          // An array of bases stored verbatim\n          const ret = data.split(',')\n          const added = String.fromCharCode(...ret)\n          seq += added\n          last_pos += added.length\n          oplen += added.length\n        } else if (code === 'B') {\n          // Single base (+ qual score)\n          seq += sub\n          last_pos++\n          oplen++\n        } else if (code === 'X') {\n          // Substitution\n          seq += sub\n          last_pos++\n          oplen++\n        } else if (code === 'D' || code === 'N') {\n          // Deletion or Ref Skip\n          last_pos += data\n          if (oplen) {\n            cigar += oplen + op\n          }\n          cigar += data + code\n          oplen = 0\n        } else if (code === 'I' || code === 'S') {\n          // Insertion or soft-clip\n          seq += data\n          if (oplen) {\n            cigar += oplen + op\n          }\n          cigar += data.length + code\n          oplen = 0\n        } else if (code === 'i') {\n          // Single base insertion\n          seq += data\n          if (oplen) {\n            cigar += oplen + op\n          }\n          cigar += `${1}I`\n          oplen = 0\n        } else if (code === 'P') {\n          // Padding\n          if (oplen) {\n            cigar += oplen + op\n          }\n          cigar += `${data}P`\n        } else if (code === 'H') {\n          // Hard clip\n          if (oplen) {\n            cigar += oplen + op\n          }\n          cigar += `${data}H`\n          oplen = 0\n        } // else q or Q\n      })\n    } else {\n      sublen = this.record.readLength - seq.length\n    }\n    if (seq.length !== this.record.readLength) {\n      sublen = this.record.readLength - seq.length\n      seq += ref.substring(last_pos - refStart, last_pos - refStart + sublen)\n\n      if (oplen && op !== 'M') {\n        cigar += oplen + op\n        oplen = 0\n      }\n      op = 'M'\n      oplen += sublen\n    }\n    if (oplen) {\n      cigar += oplen + op\n    }\n    return cigar\n  }\n\n  tags() {\n    const properties = Object.getOwnPropertyNames(\n      CramSlightlyLazyFeature.prototype,\n    )\n    return properties\n      .filter(\n        prop =>\n          prop.startsWith('_get_') &&\n          prop !== '_get_mismatches' &&\n          prop !== '_get_skips_and_dels' &&\n          prop !== '_get_cram_read_features',\n      )\n      .map(methodName => methodName.replace('_get_', ''))\n  }\n\n  id() {\n    return `${this._store.id}-${this.record.uniqueId}`\n  }\n\n  get(field: string) {\n    const methodName = `_get_${field}`\n    // @ts-ignore\n    if (this[methodName]) {\n      // @ts-ignore\n      return this[methodName]()\n    }\n    return undefined\n  }\n\n  parent(): undefined | Feature {\n    return undefined\n  }\n\n  children(): undefined | Feature[] {\n    return undefined\n  }\n\n  set(): void {}\n\n  pairedFeature() {\n    return false\n  }\n\n  _get_clipPos() {\n    const mismatches = this.get('mismatches')\n    if (mismatches.length) {\n      const record =\n        this.get('strand') === -1\n          ? mismatches[mismatches.length - 1]\n          : mismatches[0]\n      const { type, cliplen } = record\n      if (type === 'softclip' || type === 'hardclip') {\n        return cliplen\n      }\n    }\n    return 0\n  }\n\n  toJSON(): SimpleFeatureSerialized {\n    // eslint-disable-next-line @typescript-eslint/no-explicit-any\n    const tags: Record<string, any> = {}\n    this.tags().forEach((t: string) => {\n      const val = this.get(t)\n      if (val !== undefined) {\n        tags[t] = val\n      }\n    })\n\n    return {\n      ...tags,\n      name: this.get('name'),\n      type: this.get('type'),\n      uniqueId: this.id(),\n    }\n  }\n\n  _get_mismatches(): Mismatch[] {\n    const readFeatures = this.get('cram_read_features')\n    const qual = this.qualRaw()\n    if (!readFeatures) {\n      return []\n    }\n    const start = this.get('start')\n    const mismatches: Mismatch[] = []\n    readFeatures.forEach(\n      (args: {\n        code: string\n        refPos: number\n        // eslint-disable-next-line @typescript-eslint/no-explicit-any\n        data: any\n        pos: number\n        sub: string\n        ref: string\n      }) => {\n        const { code, pos, data, sub, ref } = args\n        const refPos = args.refPos - 1 - start\n        if (code === 'X') {\n          // substitution\n          mismatches.push({\n            start: refPos,\n            length: 1,\n            base: sub,\n            qual: qual?.[pos],\n            altbase: ref,\n            type: 'mismatch',\n          })\n        } else if (code === 'I') {\n          // insertion\n          mismatches.push({\n            start: refPos,\n            type: 'insertion',\n            base: `${data.length}`,\n            length: 0,\n          })\n        } else if (code === 'N') {\n          // reference skip\n          mismatches.push({\n            type: 'skip',\n            length: data,\n            start: refPos,\n            base: 'N',\n          })\n        } else if (code === 'S') {\n          // soft clip\n          const len = data.length\n          mismatches.push({\n            start: refPos,\n            type: 'softclip',\n            base: `S${len}`,\n            cliplen: len,\n            length: 1,\n          })\n        } else if (code === 'P') {\n          // padding\n        } else if (code === 'H') {\n          // hard clip\n          const len = data\n          mismatches.push({\n            start: refPos,\n            type: 'hardclip',\n            base: `H${len}`,\n            cliplen: len,\n            length: 1,\n          })\n        } else if (code === 'D') {\n          // deletion\n          mismatches.push({\n            type: 'deletion',\n            length: data,\n            start: refPos,\n            base: '*',\n          })\n        } else if (code === 'b') {\n          // stretch of bases\n        } else if (code === 'q') {\n          // stretch of qual scores\n        } else if (code === 'B') {\n          // a pair of [base, qual]\n        } else if (code === 'i') {\n          // single-base insertion\n          // insertion\n          mismatches.push({\n            start: refPos,\n            type: 'insertion',\n            base: data,\n            length: 1,\n          })\n        } else if (code === 'Q') {\n          // single quality value\n        }\n      },\n    )\n    return mismatches\n  }\n\n  _get_skips_and_dels(): Mismatch[] {\n    return this._get_mismatches()\n  }\n}\n","import { CraiIndex, IndexedCramFile } from '@gmod/cram'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { Region } from '@jbrowse/core/util/types'\nimport { checkAbortSignal } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { toArray } from 'rxjs/operators'\nimport CramSlightlyLazyFeature from './CramSlightlyLazyFeature'\n\ninterface HeaderLine {\n  tag: string\n  value: any // eslint-disable-line @typescript-eslint/no-explicit-any\n  data: HeaderLine[]\n}\ninterface Header {\n  idToName?: string[]\n  nameToId?: Record<string, number>\n  readGroups?: number[]\n}\n\nexport default class CramAdapter extends BaseFeatureDataAdapter {\n  samHeader: Header = {}\n\n  private setupP?: Promise<{\n    samHeader: Header\n    cram: any // eslint-disable-line @typescript-eslint/no-explicit-any\n    sequenceAdapter: any // eslint-disable-line @typescript-eslint/no-explicit-any\n  }>\n\n  // maps a refname to an id\n  private seqIdToRefName: string[] | undefined\n\n  // maps a seqId to original refname, passed specially to render args, to a seqid\n  private seqIdToOriginalRefName: string[] = []\n\n  public async configure() {\n    const cramLocation = readConfObject(this.config, 'cramLocation')\n    const craiLocation = readConfObject(this.config, 'craiLocation')\n    if (!cramLocation) {\n      throw new Error('missing cramLocation argument')\n    }\n    if (!craiLocation) {\n      throw new Error('missing craiLocation argument')\n    }\n\n    // eslint-disable-next-line @typescript-eslint/no-explicit-any\n    const cram: any = new IndexedCramFile({\n      cramFilehandle: openLocation(cramLocation, this.pluginManager),\n      index: new CraiIndex({\n        filehandle: openLocation(craiLocation, this.pluginManager),\n      }),\n      seqFetch: this.seqFetch.bind(this),\n      checkSequenceMD5: false,\n      fetchSizeLimit: 200_000_000, // just make this a large size to avoid hitting it\n    })\n    // instantiate the sequence adapter\n    const sequenceAdapterType = readConfObject(this.config, [\n      'sequenceAdapter',\n      'type',\n    ])\n\n    if (!this.getSubAdapter) {\n      throw new Error('Error getting subadapter')\n    }\n\n    const seqConf = readConfObject(this.config, 'sequenceAdapter')\n    const { dataAdapter: sequenceAdapter } = await this.getSubAdapter(seqConf)\n\n    if (!(sequenceAdapter instanceof BaseFeatureDataAdapter)) {\n      throw new Error(\n        `CRAM feature adapters cannot use sequence adapters of type '${sequenceAdapterType}'`,\n      )\n    }\n\n    return { cram, sequenceAdapter }\n  }\n\n  async getHeader(opts?: BaseOptions) {\n    const { cram } = await this.configure()\n    return cram.cram.getHeaderText(opts)\n  }\n\n  private async seqFetch(seqId: number, start: number, end: number) {\n    start -= 1 // convert from 1-based closed to interbase\n\n    const { sequenceAdapter } = await this.configure()\n    const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId)\n    if (!refName) {\n      return undefined\n    }\n\n    const seqChunks = await sequenceAdapter\n      .getFeatures({\n        refName,\n        start,\n        end,\n        assemblyName: '',\n      })\n      .pipe(toArray())\n      .toPromise()\n\n    const sequence = seqChunks\n      .sort((a, b) => a.get('start') - b.get('start'))\n      .map(chunk => {\n        const chunkStart = chunk.get('start')\n        const chunkEnd = chunk.get('end')\n        const trimStart = Math.max(start - chunkStart, 0)\n        const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart)\n        const trimLength = trimEnd - trimStart\n        const chunkSeq = chunk.get('seq') || chunk.get('residues')\n        return chunkSeq.substr(trimStart, trimLength)\n      })\n      .join('')\n\n    if (sequence.length !== end - start) {\n      throw new Error(\n        `sequence fetch failed: fetching ${refName}:${(\n          start - 1\n        ).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(\n          end - start\n        ).toLocaleString()}`,\n      )\n    }\n    return sequence\n  }\n\n  private async setupPre(opts?: BaseOptions) {\n    const { statusCallback = () => {} } = opts || {}\n    const configured = await this.configure()\n    statusCallback('Downloading index')\n    const { cram } = configured\n    const samHeader: HeaderLine[] = await cram.cram.getSamHeader(opts?.signal)\n\n    // use the @SQ lines in the header to figure out the\n    // mapping between ref ID numbers and names\n    const idToName: string[] = []\n    const nameToId: Record<string, number> = {}\n    samHeader\n      .filter(l => l.tag === 'SQ')\n      .forEach((sqLine, refId) => {\n        sqLine.data.forEach(item => {\n          if (item.tag === 'SN') {\n            // this is the ref name\n            const refName = item.value\n            nameToId[refName] = refId\n            idToName[refId] = refName\n          }\n        })\n      })\n\n    const readGroups = samHeader\n      .filter(l => l.tag === 'RG')\n      .map(rgLine => rgLine.data.find(item => item.tag === 'ID')?.value)\n\n    const data = { idToName, nameToId, readGroups }\n    statusCallback('')\n    this.samHeader = data\n    return { samHeader: data, ...configured }\n  }\n\n  private async setup(opts?: BaseOptions) {\n    if (!this.setupP) {\n      this.setupP = this.setupPre(opts).catch(e => {\n        this.setupP = undefined\n        throw e\n      })\n    }\n    return this.setupP\n  }\n\n  async getRefNames(opts?: BaseOptions) {\n    const { samHeader } = await this.setup(opts)\n    if (!samHeader.idToName) {\n      throw new Error('CRAM file has no header lines')\n    }\n    return samHeader.idToName\n  }\n\n  // use info from the SAM header if possible, but fall back to using\n  // the ref seq order from when the browser's refseqs were loaded\n  refNameToId(refName: string) {\n    if (this.samHeader.nameToId) {\n      return this.samHeader.nameToId[refName]\n    }\n    if (this.seqIdToRefName) {\n      return this.seqIdToRefName.indexOf(refName)\n    }\n    return undefined\n  }\n\n  // use info from the SAM header if possible, but fall back to using\n  // the ref seq order from when the browser's refseqs were loaded\n  refIdToName(refId: number) {\n    if (this.samHeader.idToName) {\n      return this.samHeader.idToName[refId]\n    }\n    if (this.seqIdToRefName) {\n      return this.seqIdToRefName[refId]\n    }\n    return undefined\n  }\n\n  refIdToOriginalName(refId: number) {\n    return this.seqIdToOriginalRefName[refId]\n  }\n\n  getFeatures(\n    region: Region & { originalRefName?: string },\n    opts?: BaseOptions,\n  ) {\n    const { signal, statusCallback = () => {} } = opts || {}\n    const { refName, start, end, originalRefName } = region\n\n    return ObservableCreate<Feature>(async observer => {\n      const { cram, sequenceAdapter } = await this.setup(opts)\n      statusCallback('Downloading alignments')\n      if (!this.seqIdToRefName) {\n        this.seqIdToRefName = await sequenceAdapter.getRefNames(opts)\n      }\n      const refId = this.refNameToId(refName)\n      if (refId !== undefined) {\n        if (originalRefName) {\n          this.seqIdToOriginalRefName[refId] = originalRefName\n        }\n        const records = await cram.getRecordsForRange(refId, start, end, opts)\n        checkAbortSignal(signal)\n        // eslint-disable-next-line @typescript-eslint/no-explicit-any\n        records.forEach((record: any) => {\n          observer.next(this.cramRecordToFeature(record))\n        })\n      } else {\n        console.warn('Unknown refName', refName)\n      }\n      statusCallback('')\n      observer.complete()\n    }, signal)\n  }\n\n  freeResources(/* { region } */): void {}\n\n  cramRecordToFeature(record: unknown) {\n    return new CramSlightlyLazyFeature(record, this)\n  }\n\n  // we return the configured fetchSizeLimit, and the bytes for the region\n  async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {\n    const bytes = await this.bytesForRegions(regions, opts)\n    const fetchSizeLimit = readConfObject(this.config, 'fetchSizeLimit')\n    return {\n      bytes,\n      fetchSizeLimit,\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[], _opts?: BaseOptions) {\n    const { cram } = await this.configure()\n    const blockResults = await Promise.all(\n      regions.map(region => {\n        const { refName, start, end } = region\n        const chrId = this.refNameToId(refName)\n        return cram.index.getEntriesForRange(chrId, start, end)\n      }),\n    )\n\n    return blockResults.flat().reduce((a, b) => a + b.sliceBytes, 0)\n  }\n}\n","/* eslint-disable no-underscore-dangle */\nimport {\n  Feature,\n  SimpleFeatureSerialized,\n} from '@jbrowse/core/util/simpleFeature'\nimport { BamRecord } from '@gmod/bam'\nimport {\n  parseCigar,\n  generateMD,\n  cigarToMismatches,\n  mdToMismatches,\n  Mismatch,\n} from './MismatchParser'\n\nimport BamAdapter from './BamAdapter'\n\nexport default class BamSlightlyLazyFeature implements Feature {\n  private cachedMD = ''\n  constructor(\n    private record: BamRecord,\n    private adapter: BamAdapter,\n    private ref?: string,\n  ) {}\n\n  _get_name() {\n    return this.record.get('name')\n  }\n\n  _get_type(): string {\n    return 'match'\n  }\n\n  _get_score(): number {\n    return this.record.get('mq')\n  }\n\n  _get_flags(): string {\n    return this.record.flags\n  }\n\n  _get_strand(): number {\n    return this.record.isReverseComplemented() ? -1 : 1\n  }\n\n  _get_pair_orientation() {\n    return this.record.isPaired() ? this.record.getPairOrientation() : undefined\n  }\n\n  _get_next_seq_id() {\n    return this.record._next_refid()\n  }\n\n  _get_seq_id() {\n    // @ts-ignore\n    return this.record._refID\n  }\n\n  _get_next_refName() {\n    return this.adapter.refIdToName(this.record._next_refid())\n  }\n\n  _get_next_segment_position() {\n    const { record, adapter } = this\n    return record.isPaired()\n      ? `${adapter.refIdToName(record._next_refid())}:${record._next_pos() + 1}`\n      : undefined\n  }\n\n  _get_seq() {\n    return this.record.getReadBases()\n  }\n\n  _get_MD() {\n    const md = this.record.get('MD') || this.cachedMD\n    if (!md) {\n      const seq = this.get('seq')\n      if (seq && this.ref) {\n        this.cachedMD = generateMD(this.ref, this.get('seq'), this.get('CIGAR'))\n        return this.cachedMD\n      }\n    }\n    return md\n  }\n\n  qualRaw() {\n    return this.record.qualRaw()\n  }\n\n  set() {}\n\n  tags() {\n    const properties = Object.getOwnPropertyNames(\n      BamSlightlyLazyFeature.prototype,\n    )\n\n    return [\n      ...new Set(\n        properties\n          .filter(\n            prop =>\n              prop.startsWith('_get_') &&\n              prop !== '_get_mismatches' &&\n              prop !== '_get_skips_and_dels' &&\n              prop !== '_get_cram_read_features' &&\n              prop !== '_get_tags' &&\n              prop !== '_get_next_seq_id' &&\n              prop !== '_get_seq_id',\n          )\n          .map(methodName => methodName.replace('_get_', ''))\n          .concat(this.record._tags()),\n      ),\n    ]\n  }\n\n  id() {\n    return `${this.adapter.id}-${this.record.id()}`\n  }\n\n  // eslint-disable-next-line @typescript-eslint/no-explicit-any\n  get(field: string): any {\n    const methodName = `_get_${field}`\n    // @ts-ignore\n    if (this[methodName]) {\n      // @ts-ignore\n      return this[methodName]()\n    }\n    return this.record.get(field)\n  }\n\n  _get_refName() {\n    return this.adapter.refIdToName(this.record.seq_id())\n  }\n\n  parent() {\n    return undefined\n  }\n\n  children() {\n    return undefined\n  }\n\n  pairedFeature() {\n    return false\n  }\n\n  toJSON(): SimpleFeatureSerialized {\n    return {\n      ...Object.fromEntries(\n        this.tags()\n          .map(t => [t, this.get(t)])\n          .filter(elt => elt[1] !== undefined),\n      ),\n      uniqueId: this.id(),\n    }\n  }\n\n  _get_skips_and_dels(\n    opts: {\n      cigarAttributeName: string\n    } = {\n      cigarAttributeName: 'CIGAR',\n    },\n  ) {\n    const { cigarAttributeName } = opts\n    let mismatches: Mismatch[] = []\n    let cigarOps: string[] = []\n\n    // parse the CIGAR tag if it has one\n    const cigarString = this.get(cigarAttributeName)\n    if (cigarString) {\n      cigarOps = parseCigar(cigarString)\n      mismatches = mismatches.concat(\n        cigarToMismatches(cigarOps, this.get('seq'), this.qualRaw()),\n      )\n    }\n    return mismatches\n  }\n\n  _get_mismatches({\n    cigarAttributeName = 'CIGAR',\n    mdAttributeName = 'MD',\n  }: {\n    cigarAttributeName?: string\n    mdAttributeName?: string\n  } = {}) {\n    let mismatches: Mismatch[] = []\n    let cigarOps: string[] = []\n\n    // parse the CIGAR tag if it has one\n    const cigarString = this.get(cigarAttributeName)\n    const seq = this.get('seq')\n    const qual = this.qualRaw()\n    if (cigarString) {\n      cigarOps = parseCigar(cigarString)\n      mismatches = mismatches.concat(cigarToMismatches(cigarOps, seq, qual))\n    }\n\n    // now let's look for CRAM or MD mismatches\n    const mdString = this.get(mdAttributeName)\n    if (mdString) {\n      mismatches = mismatches.concat(\n        mdToMismatches(mdString, cigarOps, mismatches, seq, qual),\n      )\n    }\n\n    // uniqify the mismatches\n    const seen: { [index: string]: boolean } = {}\n    return mismatches.filter(m => {\n      const key = `${m.type},${m.start},${m.length}`\n      const s = seen[key]\n      seen[key] = true\n      return !s\n    })\n  }\n\n  _get_clipPos() {\n    const cigar = this.get('CIGAR') || ''\n    return this.get('strand') === -1\n      ? +(cigar.match(/(\\d+)[SH]$/) || [])[1] || 0\n      : +(cigar.match(/^(\\d+)([SH])/) || [])[1] || 0\n  }\n}\n","import { BamFile } from '@gmod/bam'\nimport {\n  BaseFeatureDataAdapter,\n  BaseOptions,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { Region } from '@jbrowse/core/util/types'\nimport {\n  checkAbortSignal,\n  bytesForRegions,\n  updateStatus,\n} from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { Feature } from '@jbrowse/core/util/simpleFeature'\nimport { toArray } from 'rxjs/operators'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport BamSlightlyLazyFeature from './BamSlightlyLazyFeature'\n\ninterface Header {\n  idToName: string[]\n  nameToId: Record<string, number>\n}\n\nexport default class BamAdapter extends BaseFeatureDataAdapter {\n  private samHeader?: Header\n\n  private setupP?: Promise<Header>\n\n  protected configured?: Promise<{\n    bam: BamFile\n    sequenceAdapter?: BaseFeatureDataAdapter\n  }>\n\n  // derived classes may not use the same configuration so a custom\n  // configure method allows derived classes to override this behavior\n  protected async configure() {\n    if (!this.configured) {\n      const bamLocation = readConfObject(this.config, 'bamLocation')\n      const location = readConfObject(this.config, ['index', 'location'])\n      const indexType = readConfObject(this.config, ['index', 'indexType'])\n      const chunkSizeLimit = readConfObject(this.config, 'chunkSizeLimit')\n      const bam = new BamFile({\n        bamFilehandle: openLocation(bamLocation, this.pluginManager),\n        csiFilehandle:\n          indexType === 'CSI'\n            ? openLocation(location, this.pluginManager)\n            : undefined,\n        baiFilehandle:\n          indexType !== 'CSI'\n            ? openLocation(location, this.pluginManager)\n            : undefined,\n        chunkSizeLimit,\n        fetchSizeLimit: 100_000_000,\n      })\n\n      const adapterConfig = readConfObject(this.config, 'sequenceAdapter')\n      if (adapterConfig && this.getSubAdapter) {\n        this.configured = this.getSubAdapter(adapterConfig).then(\n          ({ dataAdapter }) => ({\n            bam,\n            sequenceAdapter: dataAdapter as BaseFeatureDataAdapter,\n          }),\n        )\n      } else {\n        this.configured = Promise.resolve({ bam })\n      }\n    }\n    return this.configured\n  }\n\n  async getHeader(opts?: BaseOptions) {\n    const { bam } = await this.configure()\n    return bam.getHeaderText(opts)\n  }\n\n  private async setupPre(opts?: BaseOptions) {\n    const { statusCallback = () => {} } = opts || {}\n    const { bam } = await this.configure()\n    this.samHeader = await updateStatus(\n      'Downloading index',\n      statusCallback,\n      async () => {\n        const samHeader = await bam.getHeader(opts)\n\n        // use the @SQ lines in the header to figure out the\n        // mapping between ref ref ID numbers and names\n        const idToName: string[] = []\n        const nameToId: Record<string, number> = {}\n        samHeader\n          .filter(l => l.tag === 'SQ')\n          .forEach((sqLine, refId) => {\n            sqLine.data.forEach(item => {\n              if (item.tag === 'SN') {\n                // this is the ref name\n                const refName = item.value\n                nameToId[refName] = refId\n                idToName[refId] = refName\n              }\n            })\n          })\n\n        return { idToName, nameToId }\n      },\n    )\n    return this.samHeader\n  }\n\n  private async setup(opts?: BaseOptions) {\n    if (!this.setupP) {\n      this.setupP = this.setupPre(opts).catch(e => {\n        this.setupP = undefined\n        throw e\n      })\n    }\n    return this.setupP\n  }\n\n  async getRefNames(opts?: BaseOptions) {\n    const { idToName } = await this.setup(opts)\n    return idToName\n  }\n\n  private async seqFetch(refName: string, start: number, end: number) {\n    const { sequenceAdapter } = await this.configure()\n    const refSeqStore = sequenceAdapter\n    if (!refSeqStore) {\n      return undefined\n    }\n    if (!refName) {\n      return undefined\n    }\n\n    const features = refSeqStore.getFeatures({\n      refName,\n      start,\n      end,\n      assemblyName: '',\n    })\n\n    const seqChunks = await features.pipe(toArray()).toPromise()\n\n    const trimmed: string[] = []\n    seqChunks\n      .sort((a, b) => a.get('start') - b.get('start'))\n      .forEach(chunk => {\n        const chunkStart = chunk.get('start')\n        const chunkEnd = chunk.get('end')\n        const trimStart = Math.max(start - chunkStart, 0)\n        const trimEnd = Math.min(end - chunkStart, chunkEnd - chunkStart)\n        const trimLength = trimEnd - trimStart\n        const chunkSeq = chunk.get('seq') || chunk.get('residues')\n        trimmed.push(chunkSeq.substr(trimStart, trimLength))\n      })\n\n    const sequence = trimmed.join('')\n    if (sequence.length !== end - start) {\n      throw new Error(\n        `sequence fetch failed: fetching ${refName}:${(\n          start - 1\n        ).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(\n          end - start\n        ).toLocaleString()}`,\n      )\n    }\n    return sequence\n  }\n\n  getFeatures(\n    region: Region & { originalRefName?: string },\n    opts?: BaseOptions,\n  ) {\n    const { refName, start, end, originalRefName } = region\n    const { signal, statusCallback = () => {} } = opts || {}\n    return ObservableCreate<Feature>(async observer => {\n      const { bam } = await this.configure()\n      await this.setup(opts)\n      statusCallback('Downloading alignments')\n      const records = await bam.getRecordsForRange(refName, start, end, opts)\n\n      checkAbortSignal(signal)\n\n      for (const record of records) {\n        let ref: string | undefined\n        if (!record.get('md')) {\n          ref = await this.seqFetch(\n            originalRefName || refName,\n            record.get('start'),\n            record.get('end'),\n          )\n        }\n        observer.next(new BamSlightlyLazyFeature(record, this, ref))\n      }\n      statusCallback('')\n      observer.complete()\n    }, signal)\n  }\n\n  async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {\n    const { bam } = await this.configure()\n    // this is a method to avoid calling on htsget adapters\n    // @ts-ignore\n    if (bam.index.filehandle !== '?') {\n      const bytes = await bytesForRegions(regions, bam)\n      const fetchSizeLimit = readConfObject(this.config, 'fetchSizeLimit')\n      return { bytes, fetchSizeLimit }\n    } else {\n      return super.estimateRegionsStats(regions, opts)\n    }\n  }\n\n  freeResources(/* { region } */): void {}\n\n  // depends on setup being called before the BAM constructor\n  refIdToName(refId: number): string | undefined {\n    return this.samHeader?.idToName[refId]\n  }\n}\n","import { BamFile, HtsgetFile } from '@gmod/bam'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport BamAdapter from '../BamAdapter/BamAdapter'\n\nexport default class HtsgetBamAdapter extends BamAdapter {\n  protected async configure() {\n    if (!this.configured) {\n      const htsgetBase = readConfObject(this.config, 'htsgetBase')\n      const htsgetTrackId = readConfObject(this.config, 'htsgetTrackId')\n      const bam = new HtsgetFile({\n        baseUrl: htsgetBase,\n        trackId: htsgetTrackId,\n      }) as unknown as BamFile\n\n      const adapterConfig = readConfObject(this.config, 'sequenceAdapter')\n      if (adapterConfig && this.getSubAdapter) {\n        this.configured = this.getSubAdapter(adapterConfig).then(\n          ({ dataAdapter }) => {\n            return {\n              bam,\n              sequenceAdapter: dataAdapter as BaseFeatureDataAdapter,\n            }\n          },\n        )\n      }\n      this.configured = Promise.resolve({ bam })\n    }\n    return this.configured\n  }\n}\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  TextField,\n  Typography,\n  makeStyles,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {\n    width: 300,\n  },\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n}))\n\nfunction ColorByTagDlg(props: {\n  model: { setColorScheme: Function }\n  handleClose: () => void\n}) {\n  const classes = useStyles()\n  const { model, handleClose } = props\n  const [tag, setTag] = useState('')\n  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/)\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Color by tag\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent style={{ overflowX: 'hidden' }}>\n        <div className={classes.root}>\n          <Typography>Enter tag to color by: </Typography>\n          <Typography color=\"textSecondary\">\n            Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case)\n            for minimap2 read strand, HP for haplotype, RG for read group, etc.\n          </Typography>\n\n          <TextField\n            value={tag}\n            onChange={event => {\n              setTag(event.target.value)\n            }}\n            placeholder=\"Enter tag name\"\n            inputProps={{\n              maxLength: 2,\n              'data-testid': 'color-tag-name-input',\n            }}\n            error={tag.length === 2 && !validTag}\n            helperText={tag.length === 2 && !validTag ? 'Not a valid tag' : ''}\n            autoComplete=\"off\"\n            data-testid=\"color-tag-name\"\n          />\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            style={{ marginLeft: 20 }}\n            onClick={() => {\n              model.setColorScheme({\n                type: 'tag',\n                tag,\n              })\n              handleClose()\n            }}\n            disabled={!validTag}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n\nexport default observer(ColorByTagDlg)\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  Link,\n  Paper,\n  TextField,\n  Typography,\n  makeStyles,\n} from '@material-ui/core'\n\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {\n    width: 500,\n  },\n  paper: {\n    padding: theme.spacing(2),\n    margin: theme.spacing(2),\n  },\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n  field: {\n    margin: theme.spacing(2),\n  },\n}))\n\nconst flagNames = [\n  'read paired',\n  'read mapped in proper pair',\n  'read unmapped',\n  'mate unmapped',\n  'read reverse strand',\n  'mate reverse strand',\n  'first in pair',\n  'second in pair',\n  'not primary alignment',\n  'read fails platform/vendor quality checks',\n  'read is PCR or optical duplicate',\n  'supplementary alignment',\n]\n\nfunction Bitmask(props: { flag?: number; setFlag: Function }) {\n  const { flag = 0, setFlag } = props\n  return (\n    <>\n      <TextField\n        type=\"number\"\n        value={flag}\n        onChange={event => setFlag(+event.target.value)}\n      />\n      {flagNames.map((name, index) => {\n        const val = flag & (1 << index)\n        const key = `${name}_${val}`\n        return (\n          <div key={key}>\n            <input\n              type=\"checkbox\"\n              checked={Boolean(val)}\n              onChange={event => {\n                if (event.target.checked) {\n                  setFlag(flag | (1 << index))\n                } else {\n                  setFlag(flag & ~(1 << index))\n                }\n              }}\n            />\n            <label htmlFor={key}>{name}</label>\n          </div>\n        )\n      })}\n    </>\n  )\n}\n\nfunction FilterByTagDlg(props: {\n  model: {\n    filterBy?: {\n      flagExclude: number\n      flagInclude: number\n      readName?: string\n      tagFilter?: { tag: string; value: string }\n    }\n    setFilterBy: Function\n  }\n  handleClose: () => void\n}) {\n  const { model, handleClose } = props\n  const classes = useStyles()\n  const { filterBy } = model\n  const [flagInclude, setFlagInclude] = useState(filterBy?.flagInclude)\n  const [flagExclude, setFlagExclude] = useState(filterBy?.flagExclude)\n  const [tag, setTag] = useState(filterBy?.tagFilter?.tag || '')\n  const [tagValue, setTagValue] = useState(filterBy?.tagFilter?.value || '')\n  const [readName, setReadName] = useState(filterBy?.readName || '')\n  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/)\n\n  const site = 'https://broadinstitute.github.io/picard/explain-flags.html'\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Filter options\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <Typography>\n          Set filter bitmask options. Refer to <Link href={site}>{site}</Link>{' '}\n          for details\n        </Typography>\n        <div className={classes.root}>\n          <Paper className={classes.paper} variant=\"outlined\">\n            <div style={{ display: 'flex' }}>\n              <div>\n                <Typography>Read must have ALL these flags</Typography>\n                <Bitmask flag={flagInclude} setFlag={setFlagInclude} />\n              </div>\n              <div>\n                <Typography>Read must have NONE of these flags</Typography>\n                <Bitmask flag={flagExclude} setFlag={setFlagExclude} />\n              </div>\n            </div>\n          </Paper>\n          <Paper className={classes.paper} variant=\"outlined\">\n            <Typography>\n              Filter by tag name and value. Use * in the value field to get all\n              reads containing any value for that tag. Example: filter tag name\n              SA with value * to get all split/supplementary reads. Other\n              examples include HP for haplotype, or RG for read group\n            </Typography>\n            <TextField\n              className={classes.field}\n              value={tag}\n              onChange={event => {\n                setTag(event.target.value)\n              }}\n              placeholder=\"Enter tag name\"\n              inputProps={{\n                maxLength: 2,\n                'data-testid': 'color-tag-name-input',\n              }}\n              error={tag.length === 2 && !validTag}\n              helperText={\n                tag.length === 2 && !validTag ? 'Not a valid tag' : ''\n              }\n              data-testid=\"color-tag-name\"\n            />\n            <TextField\n              className={classes.field}\n              value={tagValue}\n              onChange={event => {\n                setTagValue(event.target.value)\n              }}\n              placeholder=\"Enter tag value\"\n              inputProps={{\n                'data-testid': 'color-tag-name-input',\n              }}\n              data-testid=\"color-tag-value\"\n            />\n          </Paper>\n          <Paper className={classes.paper} variant=\"outlined\">\n            <Typography>Filter by read name</Typography>\n            <TextField\n              className={classes.field}\n              value={readName}\n              onChange={event => {\n                setReadName(event.target.value)\n              }}\n              placeholder=\"Enter read name\"\n              inputProps={{\n                'data-testid': 'color-tag-readname-input',\n              }}\n              data-testid=\"color-tag-readname\"\n            />\n          </Paper>\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            onClick={() => {\n              model.setFilterBy({\n                flagInclude,\n                flagExclude,\n                readName,\n                tagFilter:\n                  tag !== ''\n                    ? {\n                        tag,\n                        value: tagValue,\n                      }\n                    : undefined,\n              })\n              handleClose()\n            }}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n\nexport default observer(FilterByTagDlg)\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  TextField,\n  Typography,\n  makeStyles,\n} from '@material-ui/core'\n\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {\n    margin: 0,\n    padding: theme.spacing(2),\n  },\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n}))\n\nfunction SortByTagDlg(props: {\n  model: { setSortedBy: Function }\n  handleClose: () => void\n}) {\n  const classes = useStyles()\n  const { model, handleClose } = props\n  const [tag, setTag] = useState('')\n  const validTag = tag.match(/^[A-Za-z][A-Za-z0-9]$/)\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Sort by tag\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <div>\n          <Typography>Set the tag to sort by</Typography>\n          <Typography color=\"textSecondary\">\n            Examples: HP for haplotype, RG for read group, etc.\n          </Typography>\n          <TextField\n            value={tag}\n            onChange={event => {\n              setTag(event.target.value)\n            }}\n            placeholder=\"Enter tag name\"\n            inputProps={{\n              maxLength: 2,\n              'data-testid': 'sort-tag-name-input',\n            }}\n            error={tag.length === 2 && !validTag}\n            helperText={tag.length === 2 && !validTag ? 'Not a valid tag' : ''}\n            autoComplete=\"off\"\n            data-testid=\"sort-tag-name\"\n          />\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            onClick={() => {\n              model.setSortedBy('tag', tag)\n              handleClose()\n            }}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\nexport default observer(SortByTagDlg)\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  TextField,\n  Typography,\n  IconButton,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  Checkbox,\n  FormControlLabel,\n  makeStyles,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {\n    margin: theme.spacing(4),\n  },\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n}))\n\nfunction SetFeatureHeightDlg(props: {\n  model: {\n    minScore: number\n    maxScore: number\n    setMinScore: Function\n    setMaxScore: Function\n    setFeatureHeight: Function\n    setNoSpacing: Function\n    featureHeightSetting: number\n    noSpacing: boolean\n  }\n  handleClose: () => void\n}) {\n  const classes = useStyles()\n  const { model, handleClose } = props\n  const { featureHeightSetting, noSpacing: noSpacingSetting } = model\n\n  const [height, setHeight] = useState(`${featureHeightSetting}`)\n  const [noSpacing, setNoSpacing] = useState(noSpacingSetting)\n\n  const ok = height !== '' && !Number.isNaN(+height)\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Set feature height\n        <IconButton className={classes.closeButton} onClick={handleClose}>\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <Typography>\n          Adjust the feature height and whether there is any spacing between\n          features. Setting feature height to 1 and removing spacing makes the\n          display very compact\n        </Typography>\n        <div className={classes.root}>\n          <Typography>Enter feature height: </Typography>\n          <TextField\n            value={height}\n            onChange={event => {\n              setHeight(event.target.value)\n            }}\n          />\n          <FormControlLabel\n            control={\n              <Checkbox\n                checked={!!noSpacing}\n                onChange={() => setNoSpacing(val => !val)}\n              />\n            }\n            label=\"Remove spacing between features in y-direction?\"\n          />\n\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            type=\"submit\"\n            style={{ marginLeft: 20 }}\n            disabled={!ok}\n            onClick={() => {\n              model.setFeatureHeight(\n                height !== '' && !Number.isNaN(+height) ? +height : undefined,\n              )\n              model.setNoSpacing(noSpacing)\n\n              handleClose()\n            }}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n\nexport default observer(SetFeatureHeightDlg)\n","import React, { useState } from 'react'\nimport { observer } from 'mobx-react'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  TextField,\n  Typography,\n  makeStyles,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {\n    width: 500,\n  },\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n  field: {\n    margin: theme.spacing(2),\n  },\n}))\n\nfunction SetMaxHeightDlg(props: {\n  model: {\n    maxHeight?: number\n    setMaxHeight: Function\n  }\n  handleClose: () => void\n}) {\n  const { model, handleClose } = props\n  const classes = useStyles()\n  const { maxHeight = '' } = model\n  const [max, setMax] = useState(`${maxHeight}`)\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle id=\"alert-dialog-title\">\n        Filter options\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <div className={classes.root}>\n          <Typography>Set max height for the track</Typography>\n          <TextField\n            value={max}\n            onChange={event => {\n              setMax(event.target.value)\n            }}\n            placeholder=\"Enter max height for layout\"\n          />\n          <Button\n            variant=\"contained\"\n            color=\"primary\"\n            type=\"submit\"\n            style={{ marginLeft: 20 }}\n            onClick={() => {\n              model.setMaxHeight(\n                max !== '' && !Number.isNaN(+max) ? +max : undefined,\n              )\n              handleClose()\n            }}\n          >\n            Submit\n          </Button>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n\nexport default observer(SetMaxHeightDlg)\n","import React from 'react'\nimport { observer } from 'mobx-react'\nimport { ObservableMap } from 'mobx'\nimport {\n  Button,\n  Dialog,\n  DialogContent,\n  DialogTitle,\n  IconButton,\n  Typography,\n  CircularProgress,\n  makeStyles,\n} from '@material-ui/core'\nimport CloseIcon from '@material-ui/icons/Close'\n\nconst useStyles = makeStyles(theme => ({\n  root: {},\n  closeButton: {\n    position: 'absolute',\n    right: theme.spacing(1),\n    top: theme.spacing(1),\n    color: theme.palette.grey[500],\n  },\n\n  table: {\n    border: '1px solid #888',\n    margin: theme.spacing(4),\n    '& td': {\n      padding: theme.spacing(1),\n    },\n  },\n}))\n\nfunction ModificationTable({\n  modifications,\n}: {\n  modifications: [string, string][]\n}) {\n  const classes = useStyles()\n  return (\n    <table className={classes.table}>\n      <tbody>\n        {modifications.map(([key, value]) => (\n          <tr key={key}>\n            <td>{key}</td>\n            <td>{value}</td>\n            <td\n              style={{\n                width: '1em',\n                background: value,\n              }}\n            />\n          </tr>\n        ))}\n      </tbody>\n    </table>\n  )\n}\n\nfunction ColorByTagDlg(props: {\n  model: {\n    setColorScheme: Function\n    modificationTagMap: ObservableMap<string, string>\n    colorBy?: { type: string }\n  }\n  handleClose: () => void\n}) {\n  const classes = useStyles()\n  const { model, handleClose } = props\n  const { colorBy, modificationTagMap } = model\n\n  const modifications = [...modificationTagMap.entries()]\n\n  return (\n    <Dialog open onClose={handleClose}>\n      <DialogTitle>\n        Color by modifications\n        <IconButton\n          aria-label=\"close\"\n          className={classes.closeButton}\n          onClick={handleClose}\n        >\n          <CloseIcon />\n        </IconButton>\n      </DialogTitle>\n      <DialogContent>\n        <div className={classes.root}>\n          <Typography>\n            You can choose to color the modifications in the BAM/CRAM MM/ML\n            specification using this dialog. Choosing modifications colors the\n            modified positions and can color multiple modification types.\n            Choosing the methylation setting colors methylated and unmethylated\n            CpG.\n          </Typography>\n          <Typography>\n            Note: you can revisit this dialog to see the current mapping of\n            colors to modification type for the modification coloring mode\n          </Typography>\n          <div style={{ margin: 20 }}>\n            {colorBy?.type === 'modifications' ? (\n              <div>\n                {modifications.length ? (\n                  <>\n                    Current modification-type-to-color mapping\n                    <ModificationTable\n                      modifications={[...modificationTagMap.entries()]}\n                    />\n                  </>\n                ) : (\n                  <div>\n                    <Typography>\n                      Note: color by modifications is already enabled. Loading\n                      current modifications...\n                    </Typography>\n                    <CircularProgress size={15} />\n                  </div>\n                )}\n              </div>\n            ) : null}\n            {colorBy?.type === 'methylation' ? (\n              <ModificationTable\n                modifications={[\n                  ['methylated', 'red'],\n                  ['unmethylated', 'blue'],\n                ]}\n              />\n            ) : null}\n          </div>\n          <div style={{ display: 'flex' }}>\n            <Button\n              variant=\"contained\"\n              color=\"primary\"\n              style={{ margin: 5 }}\n              onClick={() => {\n                model.setColorScheme({\n                  type: 'modifications',\n                })\n                handleClose()\n              }}\n            >\n              Modifications\n            </Button>\n            <Button\n              variant=\"contained\"\n              color=\"primary\"\n              style={{ margin: 5 }}\n              onClick={() => {\n                model.setColorScheme({\n                  type: 'methylation',\n                })\n                handleClose()\n              }}\n            >\n              Methylation\n            </Button>\n            <Button\n              variant=\"contained\"\n              color=\"secondary\"\n              style={{ margin: 5 }}\n              onClick={() => handleClose()}\n            >\n              Cancel\n            </Button>\n          </div>\n        </div>\n      </DialogContent>\n    </Dialog>\n  )\n}\n\nexport default observer(ColorByTagDlg)\n","import React, { useState } from 'react'\nimport {\n  Typography,\n  Link,\n  Paper,\n  Checkbox,\n  FormControlLabel,\n  FormGroup,\n  makeStyles,\n} from '@material-ui/core'\nimport { observer } from 'mobx-react'\nimport { getSession } from '@jbrowse/core/util'\nimport copy from 'copy-to-clipboard'\nimport {\n  FeatureDetails,\n  BaseCard,\n  SimpleValue,\n} from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'\nimport { parseCigar } from '../BamAdapter/MismatchParser'\n\nconst useStyles = makeStyles(() => ({\n  compact: {\n    paddingRight: 0,\n    paddingTop: 0,\n    paddingBottom: 0,\n  },\n}))\n\nconst omit = ['clipPos', 'flags']\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction AlignmentFlags(props: { feature: any }) {\n  const classes = useStyles()\n  const { feature } = props\n  const { flags } = feature\n  const flagNames = [\n    'read paired',\n    'read mapped in proper pair',\n    'read unmapped',\n    'mate unmapped',\n    'read reverse strand',\n    'mate reverse strand',\n    'first in pair',\n    'second in pair',\n    'not primary alignment',\n    'read fails platform/vendor quality checks',\n    'read is PCR or optical duplicate',\n    'supplementary alignment',\n  ]\n  return (\n    <BaseCard {...props} title=\"Flags\">\n      <SimpleValue name={'Flag'} value={flags} />\n\n      <FormGroup>\n        {flagNames.map((name, index) => {\n          const val = flags & (1 << index)\n          const key = `${name}_${val}`\n          return (\n            <FormControlLabel\n              key={key}\n              control={\n                <Checkbox\n                  className={classes.compact}\n                  checked={Boolean(val)}\n                  name={name}\n                  readOnly\n                />\n              }\n              label={name}\n            />\n          )\n        })}\n      </FormGroup>\n    </BaseCard>\n  )\n}\n\nfunction Formatter({ value }: { value: unknown }) {\n  const [show, setShow] = useState(false)\n  const display = String(value)\n  if (display.length > 100) {\n    return (\n      <>\n        <button type=\"button\" onClick={() => copy(display)}>\n          Copy\n        </button>\n        <button type=\"button\" onClick={() => setShow(val => !val)}>\n          {show ? 'Show less' : 'Show more'}\n        </button>\n        <div>{show ? display : `${display.slice(0, 100)}...`}</div>\n      </>\n    )\n  }\n  return <div>{display}</div>\n}\n\n// utility function to get length of alignment from cigar\nfunction getLengthOnRef(cigar: string) {\n  const cigarOps = parseCigar(cigar)\n  let lengthOnRef = 0\n  for (let i = 0; i < cigarOps.length; i += 2) {\n    const len = +cigarOps[i]\n    const op = cigarOps[i + 1]\n    if (op !== 'H' && op !== 'S' && op !== 'I') {\n      lengthOnRef += len\n    }\n  }\n  return lengthOnRef\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction SupplementaryAlignments(props: { tag: string; model: any }) {\n  const { tag, model } = props\n  const session = getSession(model)\n  return (\n    <BaseCard {...props} title=\"Supplementary alignments\">\n      <Typography>List of supplementary alignment locations</Typography>\n      <ul>\n        {tag\n          .split(';')\n          .filter(SA => !!SA)\n          .map((SA, index) => {\n            const [saRef, saStart, saStrand, saCigar] = SA.split(',')\n            const saLength = getLengthOnRef(saCigar)\n            const extra = Math.floor(saLength / 5)\n            const start = +saStart\n            const end = +saStart + saLength\n            const locString = `${saRef}:${Math.max(1, start - extra)}-${\n              end + extra\n            }`\n            const displayStart = start.toLocaleString('en-US')\n            const displayEnd = end.toLocaleString('en-US')\n            const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand})`\n            return (\n              <li key={`${locString}-${index}`}>\n                <Link\n                  onClick={() => {\n                    const { view } = model\n                    try {\n                      if (view) {\n                        view.navToLocString(locString)\n                      } else {\n                        throw new Error(\n                          'No view associated with this view anymore',\n                        )\n                      }\n                    } catch (e) {\n                      console.error(e)\n                      session.notify(`${e}`)\n                    }\n                  }}\n                  href=\"#\"\n                >\n                  {displayString}\n                </Link>\n              </li>\n            )\n          })}\n      </ul>\n    </BaseCard>\n  )\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction PairLink({ locString, model }: { locString: string; model: any }) {\n  const session = getSession(model)\n  return (\n    <Link\n      onClick={() => {\n        const { view } = model\n        try {\n          if (view) {\n            view.navToLocString(locString)\n          } else {\n            session.notify(\n              'No view associated with this feature detail panel anymore',\n              'warning',\n            )\n          }\n        } catch (e) {\n          console.error(e)\n          session.notify(`${e}`)\n        }\n      }}\n      href=\"#\"\n    >\n      {locString}\n    </Link>\n  )\n}\n\n// eslint-disable-next-line @typescript-eslint/no-explicit-any\nfunction AlignmentFeatureDetails(props: { model: any }) {\n  const { model } = props\n  const feat = JSON.parse(JSON.stringify(model.featureData))\n  const SA = (feat.tags && feat.tags.SA) || feat.SA\n  return (\n    <Paper data-testid=\"alignment-side-drawer\">\n      <FeatureDetails\n        {...props}\n        omit={omit}\n        feature={feat}\n        formatter={(value: unknown, key: string) => {\n          return key === 'next_segment_position' ? (\n            <PairLink model={model} locString={value as string} />\n          ) : (\n            <Formatter value={value} />\n          )\n        }}\n      />\n      {SA ? <SupplementaryAlignments model={model} tag={SA} /> : null}\n      <AlignmentFlags feature={feat} {...props} />\n    </Paper>\n  )\n}\n\nexport default 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