scran.js/browser/wasm/scran.js

Single cell RNA-seq analysis in Javascript

// This code implements the `-sMODULARIZE` settings by taking the generated
// JS program code (INNER_JS_CODE) and wrapping it in a factory function.

// When targetting node and ES6 we use `await import ..` in the generated code
// so the outer function needs to be marked as async.
async function loadScran(moduleArg = {}) {
  var moduleRtn;

// include: shell.js
// include: minimum_runtime_check.js
// end include: minimum_runtime_check.js
// The Module object: Our interface to the outside world. We import
// and export values on it. There are various ways Module can be used:
// 1. Not defined. We create it here
// 2. A function parameter, function(moduleArg) => Promise<Module>
// 3. pre-run appended it, var Module = {}; ..generated code..
// 4. External script tag defines var Module.
// We need to check if Module already exists (e.g. case 3 above).
// Substitution will be replaced with actual code on later stage of the build,
// this way Closure Compiler will not mangle it (e.g. case 4. above).
// Note that if you want to run closure, and also to use Module
// after the generated code, you will need to define   var Module = {};
// before the code. Then that object will be used in the code, and you
// can continue to use Module afterwards as well.
var Module = moduleArg;

// Determine the runtime environment we are in. You can customize this by
// setting the ENVIRONMENT setting at compile time (see settings.js).
// Attempt to auto-detect the environment
var ENVIRONMENT_IS_WEB = !!globalThis.window;

var ENVIRONMENT_IS_WORKER = !!globalThis.WorkerGlobalScope;

// N.b. Electron.js environment is simultaneously a NODE-environment, but
// also a web environment.
var ENVIRONMENT_IS_NODE = globalThis.process?.versions?.node && globalThis.process?.type != "renderer";

// Three configurations we can be running in:
// 1) We could be the application main() thread running in the main JS UI thread. (ENVIRONMENT_IS_WORKER == false and ENVIRONMENT_IS_PTHREAD == false)
// 2) We could be the application main() thread proxied to worker. (with Emscripten -sPROXY_TO_WORKER) (ENVIRONMENT_IS_WORKER == true, ENVIRONMENT_IS_PTHREAD == false)
// 3) We could be an application pthread running in a worker. (ENVIRONMENT_IS_WORKER == true and ENVIRONMENT_IS_PTHREAD == true)
// The way we signal to a worker that it is hosting a pthread is to construct
// it with a specific name.
var ENVIRONMENT_IS_PTHREAD = ENVIRONMENT_IS_WORKER && self.name?.startsWith("em-pthread");

// --pre-jses are emitted after the Module integration code, so that they can
// refer to Module (if they choose; they can also define Module)
var arguments_ = [];

var thisProgram = "./this.program";

var quit_ = (status, toThrow) => {
  throw toThrow;
};

var _scriptName = import.meta.url;

// `/` should be present at the end if `scriptDirectory` is not empty
var scriptDirectory = "";

function locateFile(path) {
  if (Module["locateFile"]) {
    return Module["locateFile"](path, scriptDirectory);
  }
  return scriptDirectory + path;
}

// Hooks that are implemented differently in different runtime environments.
var readAsync, readBinary;

// Note that this includes Node.js workers when relevant (pthreads is enabled).
// Node.js workers are detected as a combination of ENVIRONMENT_IS_WORKER and
// ENVIRONMENT_IS_NODE.
if (ENVIRONMENT_IS_WEB || ENVIRONMENT_IS_WORKER) {
  try {
    scriptDirectory = new URL(".", _scriptName).href;
  } catch {}
  {
    // include: web_or_worker_shell_read.js
    if (ENVIRONMENT_IS_WORKER) {
      readBinary = url => {
        var xhr = new XMLHttpRequest;
        xhr.open("GET", url, false);
        xhr.responseType = "arraybuffer";
        xhr.send(null);
        return new Uint8Array(/** @type{!ArrayBuffer} */ (xhr.response));
      };
    }
    readAsync = async url => {
      var response = await fetch(url, {
        credentials: "same-origin"
      });
      if (response.ok) {
        return response.arrayBuffer();
      }
      throw new Error(response.status + " : " + response.url);
    };
  }
} else {}

var out = console.log.bind(console);

var err = console.error.bind(console);

// end include: shell.js
// include: preamble.js
// === Preamble library stuff ===
// Documentation for the public APIs defined in this file must be updated in:
//    site/source/docs/api_reference/preamble.js.rst
// A prebuilt local version of the documentation is available at:
//    site/build/text/docs/api_reference/preamble.js.txt
// You can also build docs locally as HTML or other formats in site/
// An online HTML version (which may be of a different version of Emscripten)
//    is up at http://kripken.github.io/emscripten-site/docs/api_reference/preamble.js.html
var wasmBinary;

// Wasm globals
// For sending to workers.
var wasmModule;

//========================================
// Runtime essentials
//========================================
// whether we are quitting the application. no code should run after this.
// set in exit() and abort()
var ABORT = false;

// set by exit() and abort().  Passed to 'onExit' handler.
// NOTE: This is also used as the process return code code in shell environments
// but only when noExitRuntime is false.
var EXITSTATUS;

// include: runtime_common.js
// include: runtime_stack_check.js
// end include: runtime_stack_check.js
// include: runtime_exceptions.js
// end include: runtime_exceptions.js
// include: runtime_debug.js
// end include: runtime_debug.js
// Support for growable heap + pthreads, where the buffer may change, so JS views
// must be updated.
function growMemViews() {
  // `updateMemoryViews` updates all the views simultaneously, so it's enough to check any of them.
  if (wasmMemory.buffer != HEAP8.buffer) {
    updateMemoryViews();
  }
}

var readyPromiseResolve, readyPromiseReject;

// include: runtime_pthread.js
// Pthread Web Worker handling code.
// This code runs only on pthread web workers and handles pthread setup
// and communication with the main thread via postMessage.
var startWorker;

if (ENVIRONMENT_IS_PTHREAD) {
  // Thread-local guard variable for one-time init of the JS state
  var initializedJS = false;
  // Turn unhandled rejected promises into errors so that the main thread will be
  // notified about them.
  self.onunhandledrejection = e => {
    throw e.reason || e;
  };
  function handleMessage(e) {
    try {
      var msgData = e["data"];
      //dbg('msgData: ' + Object.keys(msgData));
      var cmd = msgData.cmd;
      if (cmd === "load") {
        // Preload command that is called once per worker to parse and load the Emscripten code.
        // Until we initialize the runtime, queue up any further incoming messages.
        let messageQueue = [];
        self.onmessage = e => messageQueue.push(e);
        // And add a callback for when the runtime is initialized.
        startWorker = () => {
          // Notify the main thread that this thread has loaded.
          postMessage({
            cmd: "loaded"
          });
          // Process any messages that were queued before the thread was ready.
          for (let msg of messageQueue) {
            handleMessage(msg);
          }
          // Restore the real message handler.
          self.onmessage = handleMessage;
        };
        // Use `const` here to ensure that the variable is scoped only to
        // that iteration, allowing safe reference from a closure.
        for (const handler of msgData.handlers) {
          // The the main module has a handler for a certain even, but no
          // handler exists on the pthread worker, then proxy that handler
          // back to the main thread.
          if (!Module[handler] || Module[handler].proxy) {
            Module[handler] = (...args) => {
              postMessage({
                cmd: "callHandler",
                handler,
                args
              });
            };
            // Rebind the out / err handlers if needed
            if (handler == "print") out = Module[handler];
            if (handler == "printErr") err = Module[handler];
          }
        }
        wasmMemory = msgData.wasmMemory;
        updateMemoryViews();
        wasmModule = msgData.wasmModule;
        createWasm();
        run();
      } else if (cmd === "run") {
        // Call inside JS module to set up the stack frame for this pthread in JS module scope.
        // This needs to be the first thing that we do, as we cannot call to any C/C++ functions
        // until the thread stack is initialized.
        establishStackSpace(msgData.pthread_ptr);
        // Pass the thread address to wasm to store it for fast access.
        __emscripten_thread_init(msgData.pthread_ptr, /*is_main=*/ 0, /*is_runtime=*/ 0, /*can_block=*/ 1, 0, 0);
        PThread.threadInitTLS();
        // Await mailbox notifications with `Atomics.waitAsync` so we can start
        // using the fast `Atomics.notify` notification path.
        __emscripten_thread_mailbox_await(msgData.pthread_ptr);
        if (!initializedJS) {
          // Embind must initialize itself on all threads, as it generates support JS.
          // We only do this once per worker since they get reused
          __embind_initialize_bindings();
          initializedJS = true;
        }
        try {
          invokeEntryPoint(msgData.start_routine, msgData.arg);
        } catch (ex) {
          if (ex != "unwind") {
            // The pthread "crashed".  Do not call `_emscripten_thread_exit` (which
            // would make this thread joinable).  Instead, re-throw the exception
            // and let the top level handler propagate it back to the main thread.
            throw ex;
          }
        }
      } else if (msgData.target === "setimmediate") {} else if (cmd === "checkMailbox") {
        if (initializedJS) {
          checkMailbox();
        }
      } else if (cmd) {
        // The received message looks like something that should be handled by this message
        // handler, (since there is a cmd field present), but is not one of the
        // recognized commands:
        err(`worker: received unknown command ${cmd}`);
        err(msgData);
      }
    } catch (ex) {
      __emscripten_thread_crashed();
      throw ex;
    }
  }
  self.onmessage = handleMessage;
}

// ENVIRONMENT_IS_PTHREAD
// end include: runtime_pthread.js
// Memory management
var /** @type {!Int8Array} */ HEAP8, /** @type {!Uint8Array} */ HEAPU8, /** @type {!Int16Array} */ HEAP16, /** @type {!Uint16Array} */ HEAPU16, /** @type {!Int32Array} */ HEAP32, /** @type {!Uint32Array} */ HEAPU32, /** @type {!Float32Array} */ HEAPF32, /** @type {!Float64Array} */ HEAPF64;

// BigInt64Array type is not correctly defined in closure
var /** not-@type {!BigInt64Array} */ HEAP64, /* BigUint64Array type is not correctly defined in closure
/** not-@type {!BigUint64Array} */ HEAPU64;

var runtimeInitialized = false;

function updateMemoryViews() {
  var b = wasmMemory.buffer;
  Module["HEAP8"] = HEAP8 = new Int8Array(b);
  HEAP16 = new Int16Array(b);
  HEAPU8 = new Uint8Array(b);
  HEAPU16 = new Uint16Array(b);
  HEAP32 = new Int32Array(b);
  HEAPU32 = new Uint32Array(b);
  HEAPF32 = new Float32Array(b);
  HEAPF64 = new Float64Array(b);
  HEAP64 = new BigInt64Array(b);
  HEAPU64 = new BigUint64Array(b);
}

// In non-standalone/normal mode, we create the memory here.
// include: runtime_init_memory.js
// Create the wasm memory. (Note: this only applies if IMPORTED_MEMORY is defined)
// check for full engine support (use string 'subarray' to avoid closure compiler confusion)
function initMemory() {
  if ((ENVIRONMENT_IS_PTHREAD)) {
    return;
  }
  if (Module["wasmMemory"]) {
    wasmMemory = Module["wasmMemory"];
  } else {
    var INITIAL_MEMORY = Module["INITIAL_MEMORY"] || 16777216;
    /** @suppress {checkTypes} */ wasmMemory = new WebAssembly.Memory({
      "initial": BigInt(INITIAL_MEMORY / 65536),
      // In theory we should not need to emit the maximum if we want "unlimited"
      // or 4GB of memory, but VMs error on that atm, see
      // https://github.com/emscripten-core/emscripten/issues/14130
      // And in the pthreads case we definitely need to emit a maximum. So
      // always emit one.
      "maximum": 262144n,
      "shared": true,
      "address": "i64"
    });
  }
  updateMemoryViews();
}

// end include: runtime_init_memory.js
// include: memoryprofiler.js
// end include: memoryprofiler.js
// end include: runtime_common.js
function preRun() {
  if (Module["preRun"]) {
    if (typeof Module["preRun"] == "function") Module["preRun"] = [ Module["preRun"] ];
    while (Module["preRun"].length) {
      addOnPreRun(Module["preRun"].shift());
    }
  }
  // Begin ATPRERUNS hooks
  callRuntimeCallbacks(onPreRuns);
}

function initRuntime() {
  runtimeInitialized = true;
  if (ENVIRONMENT_IS_PTHREAD) return startWorker();
  // Begin ATINITS hooks
  if (!Module["noFSInit"] && !FS.initialized) FS.init();
  TTY.init();
  // End ATINITS hooks
  wasmExports["sa"]();
  // Begin ATPOSTCTORS hooks
  FS.ignorePermissions = false;
}

function postRun() {
  if ((ENVIRONMENT_IS_PTHREAD)) {
    return;
  }
  // PThreads reuse the runtime from the main thread.
  if (Module["postRun"]) {
    if (typeof Module["postRun"] == "function") Module["postRun"] = [ Module["postRun"] ];
    while (Module["postRun"].length) {
      addOnPostRun(Module["postRun"].shift());
    }
  }
  // Begin ATPOSTRUNS hooks
  callRuntimeCallbacks(onPostRuns);
}

/** @param {string|number=} what */ function abort(what) {
  Module["onAbort"]?.(what);
  what = "Aborted(" + what + ")";
  // TODO(sbc): Should we remove printing and leave it up to whoever
  // catches the exception?
  err(what);
  ABORT = true;
  what += ". Build with -sASSERTIONS for more info.";
  // Use a wasm runtime error, because a JS error might be seen as a foreign
  // exception, which means we'd run destructors on it. We need the error to
  // simply make the program stop.
  // FIXME This approach does not work in Wasm EH because it currently does not assume
  // all RuntimeErrors are from traps; it decides whether a RuntimeError is from
  // a trap or not based on a hidden field within the object. So at the moment
  // we don't have a way of throwing a wasm trap from JS. TODO Make a JS API that
  // allows this in the wasm spec.
  // Suppress closure compiler warning here. Closure compiler's builtin extern
  // definition for WebAssembly.RuntimeError claims it takes no arguments even
  // though it can.
  // TODO(https://github.com/google/closure-compiler/pull/3913): Remove if/when upstream closure gets fixed.
  /** @suppress {checkTypes} */ var e = new WebAssembly.RuntimeError(what);
  readyPromiseReject?.(e);
  // Throw the error whether or not MODULARIZE is set because abort is used
  // in code paths apart from instantiation where an exception is expected
  // to be thrown when abort is called.
  throw e;
}

var wasmBinaryFile;

function findWasmBinary() {
  if (Module["locateFile"]) {
    return locateFile("scran.wasm");
  }
  // Use bundler-friendly `new URL(..., import.meta.url)` pattern; works in browsers too.
  return new URL("scran.wasm", import.meta.url).href;
}

function getBinarySync(file) {
  if (file == wasmBinaryFile && wasmBinary) {
    return new Uint8Array(wasmBinary);
  }
  if (readBinary) {
    return readBinary(file);
  }
  // Throwing a plain string here, even though it not normally adviables since
  // this gets turning into an `abort` in instantiateArrayBuffer.
  throw "both async and sync fetching of the wasm failed";
}

async function getWasmBinary(binaryFile) {
  // If we don't have the binary yet, load it asynchronously using readAsync.
  if (!wasmBinary) {
    // Fetch the binary using readAsync
    try {
      var response = await readAsync(binaryFile);
      return new Uint8Array(response);
    } catch {}
  }
  // Otherwise, getBinarySync should be able to get it synchronously
  return getBinarySync(binaryFile);
}

async function instantiateArrayBuffer(binaryFile, imports) {
  try {
    var binary = await getWasmBinary(binaryFile);
    var instance = await WebAssembly.instantiate(binary, imports);
    return instance;
  } catch (reason) {
    err(`failed to asynchronously prepare wasm: ${reason}`);
    abort(reason);
  }
}

async function instantiateAsync(binary, binaryFile, imports) {
  if (!binary) {
    try {
      var response = fetch(binaryFile, {
        credentials: "same-origin"
      });
      var instantiationResult = await WebAssembly.instantiateStreaming(response, imports);
      return instantiationResult;
    } catch (reason) {
      // We expect the most common failure cause to be a bad MIME type for the binary,
      // in which case falling back to ArrayBuffer instantiation should work.
      err(`wasm streaming compile failed: ${reason}`);
      err("falling back to ArrayBuffer instantiation");
    }
  }
  return instantiateArrayBuffer(binaryFile, imports);
}

function getWasmImports() {
  assignWasmImports();
  // prepare imports
  var imports = {
    "a": wasmImports
  };
  return imports;
}

// Create the wasm instance.
// Receives the wasm imports, returns the exports.
async function createWasm() {
  // Load the wasm module and create an instance of using native support in the JS engine.
  // handle a generated wasm instance, receiving its exports and
  // performing other necessary setup
  /** @param {WebAssembly.Module=} module*/ function receiveInstance(instance, module) {
    wasmExports = instance.exports;
    wasmExports = applySignatureConversions(wasmExports);
    registerTLSInit(wasmExports["za"]);
    assignWasmExports(wasmExports);
    // We now have the Wasm module loaded up, keep a reference to the compiled module so we can post it to the workers.
    wasmModule = module;
    return wasmExports;
  }
  // Prefer streaming instantiation if available.
  function receiveInstantiationResult(result) {
    // 'result' is a ResultObject object which has both the module and instance.
    // receiveInstance() will swap in the exports (to Module.asm) so they can be called
    return receiveInstance(result["instance"], result["module"]);
  }
  var info = getWasmImports();
  // User shell pages can write their own Module.instantiateWasm = function(imports, successCallback) callback
  // to manually instantiate the Wasm module themselves. This allows pages to
  // run the instantiation parallel to any other async startup actions they are
  // performing.
  // Also pthreads and wasm workers initialize the wasm instance through this
  // path.
  if (Module["instantiateWasm"]) {
    return new Promise((resolve, reject) => {
      Module["instantiateWasm"](info, (inst, mod) => {
        resolve(receiveInstance(inst, mod));
      });
    });
  }
  if ((ENVIRONMENT_IS_PTHREAD)) {
    // Instantiate from the module that was recieved via postMessage from
    // the main thread. We can just use sync instantiation in the worker.
    var instance = new WebAssembly.Instance(wasmModule, getWasmImports());
    return receiveInstance(instance, wasmModule);
  }
  wasmBinaryFile ??= findWasmBinary();
  var result = await instantiateAsync(wasmBinary, wasmBinaryFile, info);
  var exports = receiveInstantiationResult(result);
  return exports;
}

// end include: preamble.js
// Begin JS library code
class ExitStatus {
  name="ExitStatus";
  constructor(status) {
    this.message = `Program terminated with exit(${status})`;
    this.status = status;
  }
}

var terminateWorker = worker => {
  worker.terminate();
  // terminate() can be asynchronous, so in theory the worker can continue
  // to run for some amount of time after termination.  However from our POV
  // the worker now dead and we don't want to hear from it again, so we stub
  // out its message handler here.  This avoids having to check in each of
  // the onmessage handlers if the message was coming from valid worker.
  worker.onmessage = e => {};
};

var cleanupThread = pthread_ptr => {
  var worker = PThread.pthreads[pthread_ptr];
  PThread.returnWorkerToPool(worker);
};

var callRuntimeCallbacks = callbacks => {
  while (callbacks.length > 0) {
    // Pass the module as the first argument.
    callbacks.shift()(Module);
  }
};

var onPreRuns = [];

var addOnPreRun = cb => onPreRuns.push(cb);

var runDependencies = 0;

var dependenciesFulfilled = null;

var removeRunDependency = id => {
  runDependencies--;
  Module["monitorRunDependencies"]?.(runDependencies);
  if (runDependencies == 0) {
    if (dependenciesFulfilled) {
      var callback = dependenciesFulfilled;
      dependenciesFulfilled = null;
      callback();
    }
  }
};

var addRunDependency = id => {
  runDependencies++;
  Module["monitorRunDependencies"]?.(runDependencies);
};

var spawnThread = threadParams => {
  var worker = PThread.getNewWorker();
  if (!worker) {
    // No available workers in the PThread pool.
    return 6;
  }
  PThread.runningWorkers.push(worker);
  // Add to pthreads map
  PThread.pthreads[threadParams.pthread_ptr] = worker;
  worker.pthread_ptr = threadParams.pthread_ptr;
  var msg = {
    cmd: "run",
    start_routine: threadParams.startRoutine,
    arg: threadParams.arg,
    pthread_ptr: threadParams.pthread_ptr
  };
  // Ask the worker to start executing its pthread entry point function.
  worker.postMessage(msg, threadParams.transferList);
  return 0;
};

var runtimeKeepaliveCounter = 0;

var keepRuntimeAlive = () => noExitRuntime || runtimeKeepaliveCounter > 0;

var stackSave = () => _emscripten_stack_get_current();

var stackRestore = val => __emscripten_stack_restore(val);

var stackAlloc = sz => __emscripten_stack_alloc(sz);

/** @type{function(number, (number|boolean), ...number)} */ var proxyToMainThread = (funcIndex, emAsmAddr, sync, ...callArgs) => {
  // EM_ASM proxying is done by passing a pointer to the address of the EM_ASM
  // content as `emAsmAddr`.  JS library proxying is done by passing an index
  // into `proxiedJSCallArgs` as `funcIndex`. If `emAsmAddr` is non-zero then
  // `funcIndex` will be ignored.
  // Additional arguments are passed after the first three are the actual
  // function arguments.
  // The serialization buffer contains the number of call params, and then
  // all the args here.
  // We also pass 'sync' to C separately, since C needs to look at it.
  // Allocate a buffer, which will be copied by the C code.
  // First passed parameter specifies the number of arguments to the function.
  // When BigInt support is enabled, we must handle types in a more complex
  // way, detecting at runtime if a value is a BigInt or not (as we have no
  // type info here). To do that, add a "prefix" before each value that
  // indicates if it is a BigInt, which effectively doubles the number of
  // values we serialize for proxying. TODO: pack this?
  var serializedNumCallArgs = callArgs.length * 2;
  var sp = stackSave();
  var args = stackAlloc(serializedNumCallArgs * 8);
  var b = ((args) / 8);
  for (var i = 0; i < callArgs.length; i++) {
    var arg = callArgs[i];
    if (typeof arg == "bigint") {
      // The prefix is non-zero to indicate a bigint.
      (growMemViews(), HEAP64)[b + 2 * i] = 1n;
      (growMemViews(), HEAP64)[b + 2 * i + 1] = arg;
    } else {
      // The prefix is zero to indicate a JS Number.
      (growMemViews(), HEAP64)[b + 2 * i] = 0n;
      (growMemViews(), HEAPF64)[b + 2 * i + 1] = arg;
    }
  }
  var rtn = __emscripten_run_js_on_main_thread(funcIndex, emAsmAddr, serializedNumCallArgs, args, sync);
  stackRestore(sp);
  return rtn;
};

function _proc_exit(code) {
  if (ENVIRONMENT_IS_PTHREAD) return proxyToMainThread(0, 0, 1, code);
  EXITSTATUS = code;
  if (!keepRuntimeAlive()) {
    PThread.terminateAllThreads();
    Module["onExit"]?.(code);
    ABORT = true;
  }
  quit_(code, new ExitStatus(code));
}

function exitOnMainThread(returnCode) {
  if (ENVIRONMENT_IS_PTHREAD) return proxyToMainThread(1, 0, 0, returnCode);
  _exit(returnCode);
}

/** @param {boolean|number=} implicit */ var exitJS = (status, implicit) => {
  EXITSTATUS = status;
  if (ENVIRONMENT_IS_PTHREAD) {
    // implicit exit can never happen on a pthread
    // When running in a pthread we propagate the exit back to the main thread
    // where it can decide if the whole process should be shut down or not.
    // The pthread may have decided not to exit its own runtime, for example
    // because it runs a main loop, but that doesn't affect the main thread.
    exitOnMainThread(status);
    throw "unwind";
  }
  _proc_exit(status);
};

var _exit = exitJS;

var PThread = {
  unusedWorkers: [],
  runningWorkers: [],
  tlsInitFunctions: [],
  pthreads: {},
  init() {
    if ((!(ENVIRONMENT_IS_PTHREAD))) {
      PThread.initMainThread();
    }
  },
  initMainThread() {
    var pthreadPoolSize = Module.scran_custom_nthreads;
    // Start loading up the Worker pool, if requested.
    while (pthreadPoolSize--) {
      PThread.allocateUnusedWorker();
    }
    // MINIMAL_RUNTIME takes care of calling loadWasmModuleToAllWorkers
    // in postamble_minimal.js
    addOnPreRun(async () => {
      var pthreadPoolReady = PThread.loadWasmModuleToAllWorkers();
      addRunDependency("loading-workers");
      await pthreadPoolReady;
      removeRunDependency("loading-workers");
    });
  },
  terminateAllThreads: () => {
    // Attempt to kill all workers.  Sadly (at least on the web) there is no
    // way to terminate a worker synchronously, or to be notified when a
    // worker in actually terminated.  This means there is some risk that
    // pthreads will continue to be executing after `worker.terminate` has
    // returned.  For this reason, we don't call `returnWorkerToPool` here or
    // free the underlying pthread data structures.
    for (var worker of PThread.runningWorkers) {
      terminateWorker(worker);
    }
    for (var worker of PThread.unusedWorkers) {
      terminateWorker(worker);
    }
    PThread.unusedWorkers = [];
    PThread.runningWorkers = [];
    PThread.pthreads = {};
  },
  returnWorkerToPool: worker => {
    // We don't want to run main thread queued calls here, since we are doing
    // some operations that leave the worker queue in an invalid state until
    // we are completely done (it would be bad if free() ends up calling a
    // queued pthread_create which looks at the global data structures we are
    // modifying). To achieve that, defer the free() til the very end, when
    // we are all done.
    var pthread_ptr = worker.pthread_ptr;
    delete PThread.pthreads[pthread_ptr];
    // Note: worker is intentionally not terminated so the pool can
    // dynamically grow.
    PThread.unusedWorkers.push(worker);
    PThread.runningWorkers.splice(PThread.runningWorkers.indexOf(worker), 1);
    // Not a running Worker anymore
    // Detach the worker from the pthread object, and return it to the
    // worker pool as an unused worker.
    worker.pthread_ptr = 0;
    // Finally, free the underlying (and now-unused) pthread structure in
    // linear memory.
    __emscripten_thread_free_data(pthread_ptr);
  },
  threadInitTLS() {
    // Call thread init functions (these are the _emscripten_tls_init for each
    // module loaded.
    PThread.tlsInitFunctions.forEach(f => f());
  },
  loadWasmModuleToWorker: worker => new Promise(onFinishedLoading => {
    worker.onmessage = e => {
      var d = e["data"];
      var cmd = d.cmd;
      // If this message is intended to a recipient that is not the main
      // thread, forward it to the target thread.
      if (d.targetThread && d.targetThread != _pthread_self()) {
        var targetWorker = PThread.pthreads[d.targetThread];
        if (targetWorker) {
          targetWorker.postMessage(d, d.transferList);
        } else {
          err(`Internal error! Worker sent a message "${cmd}" to target pthread ${d.targetThread}, but that thread no longer exists!`);
        }
        return;
      }
      if (cmd === "checkMailbox") {
        checkMailbox();
      } else if (cmd === "spawnThread") {
        spawnThread(d);
      } else if (cmd === "cleanupThread") {
        // cleanupThread needs to be run via callUserCallback since it calls
        // back into user code to free thread data. Without this it's possible
        // the unwind or ExitStatus exception could escape here.
        callUserCallback(() => cleanupThread(d.thread));
      } else if (cmd === "loaded") {
        worker.loaded = true;
        onFinishedLoading(worker);
      } else if (d.target === "setimmediate") {
        // Worker wants to postMessage() to itself to implement setImmediate()
        // emulation.
        worker.postMessage(d);
      } else if (cmd === "callHandler") {
        Module[d.handler](...d.args);
      } else if (cmd) {
        // The received message looks like something that should be handled by this message
        // handler, (since there is a e.data.cmd field present), but is not one of the
        // recognized commands:
        err(`worker sent an unknown command ${cmd}`);
      }
    };
    worker.onerror = e => {
      var message = "worker sent an error!";
      err(`${message} ${e.filename}:${e.lineno}: ${e.message}`);
      throw e;
    };
    // When running on a pthread, none of the incoming parameters on the module
    // object are present. Proxy known handlers back to the main thread if specified.
    var handlers = [];
    var knownHandlers = [ "onExit", "onAbort", "print", "printErr" ];
    for (var handler of knownHandlers) {
      if (Module.propertyIsEnumerable(handler)) {
        handlers.push(handler);
      }
    }
    // Ask the new worker to load up the Emscripten-compiled page. This is a heavy operation.
    worker.postMessage({
      cmd: "load",
      handlers,
      wasmMemory,
      wasmModule
    });
  }),
  async loadWasmModuleToAllWorkers() {
    // Instantiation is synchronous in pthreads.
    if (ENVIRONMENT_IS_PTHREAD) {
      return;
    }
    let pthreadPoolReady = Promise.all(PThread.unusedWorkers.map(PThread.loadWasmModuleToWorker));
    return pthreadPoolReady;
  },
  allocateUnusedWorker() {
    var worker;
    // If we're using module output, use bundler-friendly pattern.
    if (Module["mainScriptUrlOrBlob"]) {
      var pthreadMainJs = Module["mainScriptUrlOrBlob"];
      if (typeof pthreadMainJs != "string") {
        pthreadMainJs = URL.createObjectURL(pthreadMainJs);
      }
      worker = new Worker(pthreadMainJs, {
        "type": "module",
        // This is the way that we signal to the Web Worker that it is hosting
        // a pthread.
        "name": "em-pthread"
      });
    } else // We need to generate the URL with import.meta.url as the base URL of the JS file
    // instead of just using new URL(import.meta.url) because bundler's only recognize
    // the first case in their bundling step. The latter ends up producing an invalid
    // URL to import from the server (e.g., for webpack the file:// path).
    // See https://github.com/webpack/webpack/issues/12638
    worker = new Worker(new URL("scran.js", import.meta.url), {
      "type": "module",
      // This is the way that we signal to the Web Worker that it is hosting
      // a pthread.
      "name": "em-pthread"
    });
    PThread.unusedWorkers.push(worker);
  },
  getNewWorker() {
    if (PThread.unusedWorkers.length == 0) {
      // PTHREAD_POOL_SIZE_STRICT should show a warning and, if set to level `2`, return from the function.
      PThread.allocateUnusedWorker();
      PThread.loadWasmModuleToWorker(PThread.unusedWorkers[0]);
    }
    return PThread.unusedWorkers.pop();
  }
};

var onPostRuns = [];

var addOnPostRun = cb => onPostRuns.push(cb);

function establishStackSpace(pthread_ptr) {
  var stackHigh = Number((growMemViews(), HEAPU64)[(((pthread_ptr) + (88)) / 8)]);
  var stackSize = Number((growMemViews(), HEAPU64)[(((pthread_ptr) + (96)) / 8)]);
  var stackLow = stackHigh - stackSize;
  // Set stack limits used by `emscripten/stack.h` function.  These limits are
  // cached in wasm-side globals to make checks as fast as possible.
  _emscripten_stack_set_limits(stackHigh, stackLow);
  // Call inside wasm module to set up the stack frame for this pthread in wasm module scope
  stackRestore(stackHigh);
}

var wasmTableMirror = [];

var getWasmTableEntry = funcPtr => {
  // Function pointers should show up as numbers, even under wasm64, but
  // we still have some places where bigint values can flow here.
  // https://github.com/emscripten-core/emscripten/issues/18200
  funcPtr = Number(funcPtr);
  var func = wasmTableMirror[funcPtr];
  if (!func) {
    /** @suppress {checkTypes} */ wasmTableMirror[funcPtr] = func = wasmTable.get(BigInt(funcPtr));
  }
  return func;
};

var invokeEntryPoint = (ptr, arg) => {
  // An old thread on this worker may have been canceled without returning the
  // `runtimeKeepaliveCounter` to zero. Reset it now so the new thread won't
  // be affected.
  runtimeKeepaliveCounter = 0;
  // Same for noExitRuntime.  The default for pthreads should always be false
  // otherwise pthreads would never complete and attempts to pthread_join to
  // them would block forever.
  // pthreads can still choose to set `noExitRuntime` explicitly, or
  // call emscripten_unwind_to_js_event_loop to extend their lifetime beyond
  // their main function.  See comment in src/runtime_pthread.js for more.
  noExitRuntime = 0;
  // pthread entry points are always of signature 'void *ThreadMain(void *arg)'
  // Native codebases sometimes spawn threads with other thread entry point
  // signatures, such as void ThreadMain(void *arg), void *ThreadMain(), or
  // void ThreadMain().  That is not acceptable per C/C++ specification, but
  // x86 compiler ABI extensions enable that to work. If you find the
  // following line to crash, either change the signature to "proper" void
  // *ThreadMain(void *arg) form, or try linking with the Emscripten linker
  // flag -sEMULATE_FUNCTION_POINTER_CASTS to add in emulation for this x86
  // ABI extension.
  var result = (a1 => getWasmTableEntry(ptr).call(null, BigInt(a1)))(arg);
  function finish(result) {
    // In MINIMAL_RUNTIME the noExitRuntime concept does not apply to
    // pthreads. To exit a pthread with live runtime, use the function
    // emscripten_unwind_to_js_event_loop() in the pthread body.
    if (keepRuntimeAlive()) {
      EXITSTATUS = result;
      return;
    }
    __emscripten_thread_exit(result);
  }
  finish(result);
};

var noExitRuntime = true;

var registerTLSInit = tlsInitFunc => PThread.tlsInitFunctions.push(tlsInitFunc);

var wasmMemory;

class ExceptionInfo {
  // excPtr - Thrown object pointer to wrap. Metadata pointer is calculated from it.
  constructor(excPtr) {
    this.excPtr = excPtr;
    this.ptr = excPtr - 48;
  }
  set_type(type) {
    (growMemViews(), HEAPU64)[(((this.ptr) + (8)) / 8)] = BigInt(type);
  }
  get_type() {
    return Number((growMemViews(), HEAPU64)[(((this.ptr) + (8)) / 8)]);
  }
  set_destructor(destructor) {
    (growMemViews(), HEAPU64)[(((this.ptr) + (16)) / 8)] = BigInt(destructor);
  }
  get_destructor() {
    return Number((growMemViews(), HEAPU64)[(((this.ptr) + (16)) / 8)]);
  }
  set_caught(caught) {
    caught = caught ? 1 : 0;
    (growMemViews(), HEAP8)[(this.ptr) + (24)] = caught;
  }
  get_caught() {
    return (growMemViews(), HEAP8)[(this.ptr) + (24)] != 0;
  }
  set_rethrown(rethrown) {
    rethrown = rethrown ? 1 : 0;
    (growMemViews(), HEAP8)[(this.ptr) + (25)] = rethrown;
  }
  get_rethrown() {
    return (growMemViews(), HEAP8)[(this.ptr) + (25)] != 0;
  }
  // Initialize native structure fields. Should be called once after allocated.
  init(type, destructor) {
    this.set_adjusted_ptr(0);
    this.set_type(type);
    this.set_destructor(destructor);
  }
  set_adjusted_ptr(adjustedPtr) {
    (growMemViews(), HEAPU64)[(((this.ptr) + (32)) / 8)] = BigInt(adjustedPtr);
  }
  get_adjusted_ptr() {
    return Number((growMemViews(), HEAPU64)[(((this.ptr) + (32)) / 8)]);
  }
}

var exceptionLast = 0;

var uncaughtExceptionCount = 0;

var INT53_MAX = 9007199254740992;

var INT53_MIN = -9007199254740992;

var bigintToI53Checked = num => (num < INT53_MIN || num > INT53_MAX) ? NaN : Number(num);

function ___cxa_throw(ptr, type, destructor) {
  ptr = bigintToI53Checked(ptr);
  type = bigintToI53Checked(type);
  destructor = bigintToI53Checked(destructor);
  var info = new ExceptionInfo(ptr);
  // Initialize ExceptionInfo content after it was allocated in __cxa_allocate_exception.
  info.init(type, destructor);
  exceptionLast = ptr;
  uncaughtExceptionCount++;
  throw exceptionLast;
}

function pthreadCreateProxied(pthread_ptr, attr, startRoutine, arg) {
  if (ENVIRONMENT_IS_PTHREAD) return proxyToMainThread(2, 0, 1, pthread_ptr, attr, startRoutine, arg);
  return ___pthread_create_js(pthread_ptr, attr, startRoutine, arg);
}

var _emscripten_has_threading_support = () => !!globalThis.SharedArrayBuffer;

function ___pthread_create_js(pthread_ptr, attr, startRoutine, arg) {
  pthread_ptr = bigintToI53Checked(pthread_ptr);
  attr = bigintToI53Checked(attr);
  startRoutine = bigintToI53Checked(startRoutine);
  arg = bigintToI53Checked(arg);
  if (!_emscripten_has_threading_support()) {
    return 6;
  }
  // List of JS objects that will transfer ownership to the Worker hosting the thread
  var transferList = [];
  var error = 0;
  // Synchronously proxy the thread creation to main thread if possible. If we
  // need to transfer ownership of objects, then proxy asynchronously via
  // postMessage.
  if (ENVIRONMENT_IS_PTHREAD && (transferList.length === 0 || error)) {
    return pthreadCreateProxied(pthread_ptr, attr, startRoutine, arg);
  }
  // If on the main thread, and accessing Canvas/OffscreenCanvas failed, abort
  // with the detected error.
  if (error) return error;
  var threadParams = {
    startRoutine,
    pthread_ptr,
    arg,
    transferList
  };
  if (ENVIRONMENT_IS_PTHREAD) {
    // The prepopulated pool of web workers that can host pthreads is stored
    // in the main JS thread. Therefore if a pthread is attempting to spawn a
    // new thread, the thread creation must be deferred to the main JS thread.
    threadParams.cmd = "spawnThread";
    postMessage(threadParams, transferList);
    // When we defer thread creation this way, we have no way to detect thread
    // creation synchronously today, so we have to assume success and return 0.
    return 0;
  }
  // We are the main thread, so we have the pthread warmup pool in this
  // thread and can fire off JS thread creation directly ourselves.
  return spawnThread(threadParams);
}

var PATH = {
  isAbs: path => path.charAt(0) === "/",
  splitPath: filename => {
    var splitPathRe = /^(\/?|)([\s\S]*?)((?:\.{1,2}|[^\/]+?|)(\.[^.\/]*|))(?:[\/]*)$/;
    return splitPathRe.exec(filename).slice(1);
  },
  normalizeArray: (parts, allowAboveRoot) => {
    // if the path tries to go above the root, `up` ends up > 0
    var up = 0;
    for (var i = parts.length - 1; i >= 0; i--) {
      var last = parts[i];
      if (last === ".") {
        parts.splice(i, 1);
      } else if (last === "..") {
        parts.splice(i, 1);
        up++;
      } else if (up) {
        parts.splice(i, 1);
        up--;
      }
    }
    // if the path is allowed to go above the root, restore leading ..s
    if (allowAboveRoot) {
      for (;up; up--) {
        parts.unshift("..");
      }
    }
    return parts;
  },
  normalize: path => {
    var isAbsolute = PATH.isAbs(path), trailingSlash = path.slice(-1) === "/";
    // Normalize the path
    path = PATH.normalizeArray(path.split("/").filter(p => !!p), !isAbsolute).join("/");
    if (!path && !isAbsolute) {
      path = ".";
    }
    if (path && trailingSlash) {
      path += "/";
    }
    return (isAbsolute ? "/" : "") + path;
  },
  dirname: path => {
    var result = PATH.splitPath(path), root = result[0], dir = result[1];
    if (!root && !dir) {
      // No dirname whatsoever
      return ".";
    }
    if (dir) {
      // It has a dirname, strip trailing slash
      dir = dir.slice(0, -1);
    }
    return root + dir;
  },
  basename: path => path && path.match(/([^\/]+|\/)\/*$/)[1],
  join: (...paths) => PATH.normalize(paths.join("/")),
  join2: (l, r) => PATH.normalize(l + "/" + r)
};

var initRandomFill = () => view => view.set(crypto.getRandomValues(new Uint8Array(view.byteLength)));

var randomFill = view => {
  // Lazily init on the first invocation.
  (randomFill = initRandomFill())(view);
};

var PATH_FS = {
  resolve: (...args) => {
    var resolvedPath = "", resolvedAbsolute = false;
    for (var i = args.length - 1; i >= -1 && !resolvedAbsolute; i--) {
      var path = (i >= 0) ? args[i] : FS.cwd();
      // Skip empty and invalid entries
      if (typeof path != "string") {
        throw new TypeError("Arguments to path.resolve must be strings");
      } else if (!path) {
        return "";
      }
      resolvedPath = path + "/" + resolvedPath;
      resolvedAbsolute = PATH.isAbs(path);
    }
    // At this point the path should be resolved to a full absolute path, but
    // handle relative paths to be safe (might happen when process.cwd() fails)
    resolvedPath = PATH.normalizeArray(resolvedPath.split("/").filter(p => !!p), !resolvedAbsolute).join("/");
    return ((resolvedAbsolute ? "/" : "") + resolvedPath) || ".";
  },
  relative: (from, to) => {
    from = PATH_FS.resolve(from).slice(1);
    to = PATH_FS.resolve(to).slice(1);
    function trim(arr) {
      var start = 0;
      for (;start < arr.length; start++) {
        if (arr[start] !== "") break;
      }
      var end = arr.length - 1;
      for (;end >= 0; end--) {
        if (arr[end] !== "") break;
      }
      if (start > end) return [];
      return arr.slice(start, end - start + 1);
    }
    var fromParts = trim(from.split("/"));
    var toParts = trim(to.split("/"));
    var length = Math.min(fromParts.length, toParts.length);
    var samePartsLength = length;
    for (var i = 0; i < length; i++) {
      if (fromParts[i] !== toParts[i]) {
        samePartsLength = i;
        break;
      }
    }
    var outputParts = [];
    for (var i = samePartsLength; i < fromParts.length; i++) {
      outputParts.push("..");
    }
    outputParts = outputParts.concat(toParts.slice(samePartsLength));
    return outputParts.join("/");
  }
};

var UTF8Decoder = globalThis.TextDecoder && new TextDecoder;

var findStringEnd = (heapOrArray, idx, maxBytesToRead, ignoreNul) => {
  var maxIdx = idx + maxBytesToRead;
  if (ignoreNul) return maxIdx;
  // TextDecoder needs to know the byte length in advance, it doesn't stop on
  // null terminator by itself.
  // As a tiny code save trick, compare idx against maxIdx using a negation,
  // so that maxBytesToRead=undefined/NaN means Infinity.
  while (heapOrArray[idx] && !(idx >= maxIdx)) ++idx;
  return idx;
};

/**
     * Given a pointer 'idx' to a null-terminated UTF8-encoded string in the given
     * array that contains uint8 values, returns a copy of that string as a
     * Javascript String object.
     * heapOrArray is either a regular array, or a JavaScript typed array view.
     * @param {number=} idx
     * @param {number=} maxBytesToRead
     * @param {boolean=} ignoreNul - If true, the function will not stop on a NUL character.
     * @return {string}
     */ var UTF8ArrayToString = (heapOrArray, idx = 0, maxBytesToRead, ignoreNul) => {
  var endPtr = findStringEnd(heapOrArray, idx, maxBytesToRead, ignoreNul);
  // When using conditional TextDecoder, skip it for short strings as the overhead of the native call is not worth it.
  if (endPtr - idx > 16 && heapOrArray.buffer && UTF8Decoder) {
    return UTF8Decoder.decode(heapOrArray.buffer instanceof ArrayBuffer ? heapOrArray.subarray(idx, endPtr) : heapOrArray.slice(idx, endPtr));
  }
  var str = "";
  while (idx < endPtr) {
    // For UTF8 byte structure, see:
    // http://en.wikipedia.org/wiki/UTF-8#Description
    // https://www.ietf.org/rfc/rfc2279.txt
    // https://tools.ietf.org/html/rfc3629
    var u0 = heapOrArray[idx++];
    if (!(u0 & 128)) {
      str += String.fromCharCode(u0);
      continue;
    }
    var u1 = heapOrArray[idx++] & 63;
    if ((u0 & 224) == 192) {
      str += String.fromCharCode(((u0 & 31) << 6) | u1);
      continue;
    }
    var u2 = heapOrArray[idx++] & 63;
    if ((u0 & 240) == 224) {
      u0 = ((u0 & 15) << 12) | (u1 << 6) | u2;
    } else {
      u0 = ((u0 & 7) << 18) | (u1 << 12) | (u2 << 6) | (heapOrArray[idx++] & 63);
    }
    if (u0 < 65536) {
      str += String.fromCharCode(u0);
    } else {
      var ch = u0 - 65536;
      str += String.fromCharCode(55296 | (ch >> 10), 56320 | (ch & 1023));
    }
  }
  return str;
};

var FS_stdin_getChar_buffer = [];

var lengthBytesUTF8 = str => {
  var len = 0;
  for (var i = 0; i < str.length; ++i) {
    // Gotcha: charCodeAt returns a 16-bit word that is a UTF-16 encoded code
    // unit, not a Unicode code point of the character! So decode
    // UTF16->UTF32->UTF8.
    // See http://unicode.org/faq/utf_bom.html#utf16-3
    var c = str.charCodeAt(i);
    // possibly a lead surrogate
    if (c <= 127) {
      len++;
    } else if (c <= 2047) {
      len += 2;
    } else if (c >= 55296 && c <= 57343) {
      len += 4;
      ++i;
    } else {
      len += 3;
    }
  }
  return len;
};

var stringToUTF8Array = (str, heap, outIdx, maxBytesToWrite) => {
  // Parameter maxBytesToWrite is not optional. Negative values, 0, null,
  // undefined and false each don't write out any bytes.
  if (!(maxBytesToWrite > 0)) return 0;
  var startIdx = outIdx;
  var endIdx = outIdx + maxBytesToWrite - 1;
  // -1 for string null terminator.
  for (var i = 0; i < str.length; ++i) {
    // For UTF8 byte structure, see http://en.wikipedia.org/wiki/UTF-8#Description
    // and https://www.ietf.org/rfc/rfc2279.txt
    // and https://tools.ietf.org/html/rfc3629
    var u = str.codePointAt(i);
    if (u <= 127) {
      if (outIdx >= endIdx) break;
      heap[outIdx++] = u;
    } else if (u <= 2047) {
      if (outIdx + 1 >= endIdx) break;
      heap[outIdx++] = 192 | (u >> 6);
      heap[outIdx++] = 128 | (u & 63);
    } else if (u <= 65535) {
      if (outIdx + 2 >= endIdx) break;
      heap[outIdx++] = 224 | (u >> 12);
      heap[outIdx++] = 128 | ((u >> 6) & 63);
      heap[outIdx++] = 128 | (u & 63);
    } else {
      if (outIdx + 3 >= endIdx) break;
      heap[outIdx++] = 240 | (u >> 18);
      heap[outIdx++] = 128 | ((u >> 12) & 63);
      heap[outIdx++] = 128 | ((u >> 6) & 63);
      heap[outIdx++] = 128 | (u & 63);
      // Gotcha: if codePoint is over 0xFFFF, it is represented as a surrogate pair in UTF-16.
      // We need to manually skip over the second code unit for correct iteration.
      i++;
    }
  }
  // Null-terminate the pointer to the buffer.
  heap[outIdx] = 0;
  return outIdx - startIdx;
};

/** @type {function(string, boolean=, number=)} */ var intArrayFromString = (stringy, dontAddNull, length) => {
  var len = length > 0 ? length : lengthBytesUTF8(stringy) + 1;
  var u8array = new Array(len);
  var numBytesWritten = stringToUTF8Array(stringy, u8array, 0, u8array.length);
  if (dontAddNull) u8array.length = numBytesWritten;
  return u8array;
};

var FS_stdin_getChar = () => {
  if (!FS_stdin_getChar_buffer.length) {
    var result = null;
    if (globalThis.window?.prompt) {
      // Browser.
      result = window.prompt("Input: ");
      // returns null on cancel
      if (result !== null) {
        result += "\n";
      }
    } else {}
    if (!result) {
      return null;
    }
    FS_stdin_getChar_buffer = intArrayFromString(result, true);
  }
  return FS_stdin_getChar_buffer.shift();
};

var TTY = {
  ttys: [],
  init() {},
  shutdown() {},
  register(dev, ops) {
    TTY.ttys[dev] = {
      input: [],
      output: [],
      ops
    };
    FS.registerDevice(dev, TTY.stream_ops);
  },
  stream_ops: {
    open(stream) {
      var tty = TTY.ttys[stream.node.rdev];
      if (!tty) {
        throw new FS.ErrnoError(43);
      }
      stream.tty = tty;
      stream.seekable = false;
    },
    close(stream) {
      // flush any pending line data
      stream.tty.ops.fsync(stream.tty);
    },
    fsync(stream) {
      stream.tty.ops.fsync(stream.tty);
    },
    read(stream, buffer, offset, length, pos) {
      if (!stream.tty || !stream.tty.ops.get_char) {
        throw new FS.ErrnoError(60);
      }
      var bytesRead = 0;
      for (var i = 0; i < length; i++) {
        var result;
        try {
          result = stream.tty.ops.get_char(stream.tty);
        } catch (e) {
          throw new FS.ErrnoError(29);
        }
        if (result === undefined && bytesRead === 0) {
          throw new FS.ErrnoError(6);
        }
        if (result === null || result === undefined) break;
        bytesRead++;
        buffer[offset + i] = result;
      }
      if (bytesRead) {
        stream.node.atime = Date.now();
      }
      return bytesRead;
    },
    write(stream, buffer, offset, length, pos) {
      if (!stream.tty || !stream.tty.ops.put_char) {
        throw new FS.ErrnoError(60);
      }
      try {
        for (var i = 0; i < length; i++) {
          stream.tty.ops.put_char(stream.tty, buffer[offset + i]);
        }
      } catch (e) {
        throw new FS.ErrnoError(29);
      }
      if (length) {
        stream.node.mtime = stream.node.ctime = Date.now();
      }
      return i;
    }
  },
  default_tty_ops: {
    get_char(tty) {
      return FS_stdin_getChar();
    },
    put_char(tty, val) {
      if (val === null || val === 10) {
        out(UTF8ArrayToString(tty.output));
        tty.output = [];
      } else {
        if (val != 0) tty.output.push(val);
      }
    },
    fsync(tty) {
      if (tty.output?.length > 0) {
        out(UTF8ArrayToString(tty.output));
        tty.output = [];
      }
    },
    ioctl_tcgets(tty) {
      // typical setting
      return {
        c_iflag: 25856,
        c_oflag: 5,
        c_cflag: 191,
        c_lflag: 35387,
        c_