int addInFileAndClose(char *firstLine, char *filename) {
FILE *fptmp;
FILE *fp;
char buffer[BUFF_DEFAULT_SIZE];
if ((fptmp = fopen(TEMP_FILE_PATH, "w")) == NULL) {
exitWithError();
}
if ((fp = fopen(filename, "r")) == NULL) {
exitWithError();
}
if (fputs(firstLine, fptmp) == EOF) {
exitWithError();
}
while (fgets(buffer, BUFF_DEFAULT_SIZE, fp) != NULL) {
fputs(buffer, fptmp);
}
fclose(fptmp);
fclose(fp);
if (remove(filename) != 0) {
exitWithError();
}
if (rename(TEMP_FILE_PATH, filename) < 0) {
exitWithError();
}
return 0;
}
void connectToSwitch(Switch *switchTrans, BankAuthorizer *autorizer) {
struct sockaddr_in switchAddress;
struct hostent *switchHost;
// creo el scoket para conectarme
switchTrans->fd = socket(AF_INET, SOCK_STREAM, 0);
if (switchTrans->fd < 0) {
exitWithError();
}
// La dirección a la cual conectarse
switchHost = gethostbyname(switchTrans->host);
switchAddress.sin_family = AF_INET;
switchAddress.sin_port = htons(switchTrans->port);
bcopy((char *) switchHost->h_addr, (char *) &switchAddress.sin_addr.s_addr,
switchHost->h_length);
// me conecto al server
if (connect(switchTrans->fd, (struct sockaddr*) &switchAddress,
(socklen_t) sizeof(struct sockaddr_in)) < 0) {
puts("Error conectandose al servidor");
exitWithError();
}
if (!authenticateBank(switchTrans, autorizer)) {
printf("Error de autenticación");
exit(EXIT_FAILURE);
}
sendServicePortToSwitch(switchTrans);
}
void mapThreadsSpawn (Parameters *P, ReadAlignChunk** RAchunk) {
for (int ithread=1;ithread<P->runThreadN;ithread++) {//spawn threads
int threadStatus=pthread_create(&g_threadChunks.threadArray[ithread], NULL, &g_threadChunks.threadRAprocessChunks, (void *) RAchunk[ithread]);
if (threadStatus>0) {//something went wrong with one of threads
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: phtread error while creating thread # " << ithread <<", error code: "<<threadStatus ;
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, 1, *P);
};
pthread_mutex_lock(&g_threadChunks.mutexLogMain);
P->inOut->logMain << "Created thread # " <<ithread <<"\n"<<flush;
pthread_mutex_unlock(&g_threadChunks.mutexLogMain);
};
RAchunk[0]->processChunks(); //start main thread
for (int ithread=1;ithread<P->runThreadN;ithread++) {//wait for all threads to complete
int threadStatus = pthread_join(g_threadChunks.threadArray[ithread], NULL);
if (threadStatus>0) {//something went wrong with one of threads
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: phtread error while joining thread # " << ithread <<", error code: "<<threadStatus ;
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, 1, *P);
};
pthread_mutex_lock(&g_threadChunks.mutexLogMain);
P->inOut->logMain << "Joined thread # " <<ithread <<"\n"<<flush;
pthread_mutex_unlock(&g_threadChunks.mutexLogMain);
};
};
uint genomeScanFastaFiles (Parameters *P, char* G, bool flagRun) {//scans fasta files. flagRun=false: check and find full size, flaRun=true: collect all the data
uint N=0;//total number of bases in the genome, including chr "spacers"
if (!flagRun && P->chrLength.size()>0)
{//previous chr records exist
P->chrStart.pop_back();//remove last record, it will be recorded again
N = P->chrStart.back()+P->chrLength.back();
P->chrLength.pop_back();//remove last record, it will be recorded again
};
ifstream fileIn;
for (uint ii=0;ii<P->genomeFastaFiles.size();ii++) {//all the input files
fileIn.open(P->genomeFastaFiles.at(ii).c_str());
if ( !fileIn.good() )
{//
ostringstream errOut;
errOut << "EXITING because of INPUT ERROR: could not open genomeFastaFile: " <<P->genomeFastaFiles.at(ii) <<"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
char cc=fileIn.peek();
if ( !fileIn.good() )
{//
ostringstream errOut;
errOut << "EXITING because of INPUT ERROR: could not read from genomeFastaFile: " <<P->genomeFastaFiles.at(ii) <<"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
if (cc!='>')
{
ostringstream errOut;
errOut << "EXITING because of INPUT ERROR: the file format of the genomeFastaFile: " <<P->genomeFastaFiles.at(ii) << "is not fasta:";
errOut << " the first character is " <<cc<<" , not > .\n";
errOut << " Solution: check formatting of the fasta file. Make sure the file is uncompressed (unzipped).\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
}; while(!fileIn.eof()) {//read each file until eof
string lineIn (4096,'.');
getline(fileIn,lineIn);
if (lineIn[0]=='>') {//new chromosome
if (!flagRun) {
istringstream lineInStream (lineIn);
lineInStream.ignore(1,' ');
string chrName1;
lineInStream >> chrName1;
P->chrName.push_back(chrName1);
};
if (!flagRun && P->chrStart.size()>0) P->chrLength.push_back(N-P->chrStart.at(P->chrStart.size()-1)); //true length of the chr
if (N>0) {//pad the chromosomes to bins boudnaries
N = ( (N+1)/P->genomeChrBinNbases+1 )*P->genomeChrBinNbases;
};
if (!flagRun) {
P->chrStart.push_back(N);
P->inOut->logMain << P->genomeFastaFiles.at(ii)<<" : chr # " << P->chrStart.size()-1 << " \""<<P->chrName.at(P->chrStart.size()-1)<<"\" chrStart: "<<N<<"\n"<<flush;
};
} else {//char lines
if (flagRun) lineIn.copy(G+N,lineIn.size(),0);
N += lineIn.size();
};
};
int main(int argc, char *argv[])
{
int sock; /* Socket */
struct sockaddr_in echoServAddr; /* Local address */
struct sockaddr_in echoClntAddr; /* Client address */
unsigned int cliAddrLen; /* Length of incoming message */
char echoBuffer[ECHOMAX]; /* Buffer for echo string */
unsigned short echoServPort; /* Server port */
int recvMsgSize; /* Size of received message */
if (argc != 2) /* Test for correct number of parameters */
{
fprintf(stderr,"Usage: %s <UDP SERVER PORT>\n", argv[0]);
exit(1);
}
echoServPort = atoi(argv[1]); /* First arg: local port */
/* Create socket for sending/receiving datagrams */
if ((sock = socket(PF_INET, SOCK_DGRAM, IPPROTO_UDP)) < 0)
exitWithError("socket() failed");
/* Construct local address structure */
memset(&echoServAddr, 0, sizeof(echoServAddr)); /* Zero out structure */
echoServAddr.sin_family = AF_INET; /* Internet address family */
echoServAddr.sin_addr.s_addr = htonl(INADDR_ANY); /* Any incoming interface */
echoServAddr.sin_port = htons(echoServPort); /* Local port */
/* Bind to the local address */
if (bind(sock, (struct sockaddr *) &echoServAddr, sizeof(echoServAddr)) < 0)
exitWithError("bind() failed");
for (;;) /* Run forever */
{
/* Set the size of the in-out parameter */
cliAddrLen = sizeof(echoClntAddr);
/* Block until receive message from a client */
if ((recvMsgSize = recvfrom(sock,
echoBuffer,
ECHOMAX,
0,
(struct sockaddr *) &echoClntAddr,
&cliAddrLen)
) < 0)
exitWithError("recvfrom() failed");
printf("Handling client %s\n", inet_ntoa(echoClntAddr.sin_addr));
// Create thread to handle client
std::thread clientThread(handleClient, echoBuffer, sock, recvMsgSize, echoClntAddr);
// Let the thread run independently
clientThread.detach();
}
/* NOT REACHED */
}
bool ScriptReaderBase::exitWithError(const io::stringc &Message, bool AppendTokenPos)
{
if (AppendTokenPos && Tkn_)
return exitWithError(Message, Tkn_);
io::Log::error(Message);
return false;
}
int changeAmmount(CreditCard *creditCard, float ammout) {
FILE *fp;
char buffer[BUFF_DEFAULT_SIZE];
char path[BUFF_DEFAULT_SIZE];
float balance = 0;
sprintf(path, "./%s",
creditCard->number);
if ((fp = fopen(path, "r")) == NULL) {
//exitWithError();
return -1;
}
if (fgets(buffer, BUFF_DEFAULT_SIZE, fp) < 0) {
exitWithError();
}
char *s = strtok(buffer, ":\n");
s = strtok(NULL, ":\n");
s = strtok(NULL, ":\n");
balance = atof(s);
if (balance + ammout < 0) {
return -1;
}
sprintf(buffer, "%s:%.2f:%.2f\n", ammout >= 0 ? "CRE" : "DEB", ammout,
balance + ammout);
fclose(fp);
return addInFileAndClose(buffer, path);
}
void sendServicePortToSwitch(Switch *switchTrans) {
char buffer[BUFF_DEFAULT_SIZE];
sprintf(buffer, "%d", DEFAULT_BANK_PORT);
if (write(switchTrans->fd, buffer, strlen(buffer) + 1) < 0) {
exitWithError();
}
}
bool ScriptReaderBase::validateBrackets()
{
const SToken* InvalidToken = 0;
switch (TokenStream_->validateBrackets(InvalidToken))
{
case VALIDATION_ERROR_UNEXPECTED:
return exitWithError("Unexpected bracket token", InvalidToken);
case VALIDATION_ERROR_UNCLOSED:
return exitWithError("Unclosed brackets", InvalidToken);
default:
break;
}
return true;
}
/* Creates Distributed Block Cyclic Layout Matrix
Requires:
- p * q = size of communication group
- m % p*bm == 0
- n % q*bn == 0
*/
void dist_matrix_init(MPI_Comm comm, struct dbcl_t *mat,
int p, int q,
int bm, int bn,
int m, int n,
double (*f)(int i, int j)) {
int rank, size;
MPI_Comm_rank(comm, &rank);
MPI_Comm_size(comm, &size);
assert(p*q == size);
assert(m % p*bm == 0);
assert(n % q*bn == 0);
// M,N are the number of blocks
int gM = m / bm;
int gN = n / bn;
int lM = gM / p;
int lN = gN / q;
// Initialize datastructure
MPI_Comm_dup(comm, &(mat->comm));
mat->p = p; mat->q = q;
mat->lM = lM; mat->lN = lN;
mat->bm = bm; mat->bn = bn;
mat->m = m; mat->n = n;
mat->value = malloc(sizeof(double) * (bm * bn) * (lM * lN));
if (mat->value == NULL)
exitWithError("dist_matrix_init: malloc failed ( mat->value )");
// Fill matrix will values supplied from function f(i, j)
int lbi, lbj;
for ( lbj=0; lbj<lN; lbj++ ) {
for ( lbi=0; lbi<lM; lbi++ ) {
int block_offset = (lbi + lbj * lM) * (bm * bn);
int i, j;
for (i=0; i<bm; i++ ) {
for (j=0; j<bn; j++ ) {
int gi = (rank % p) * bm + lbi * (p * bm) + i;
int gj = (rank / p) * bn + lbj * (q * bn) + j;
int offset = i + (j * bm);
if (gi < m && gj < n) {
mat->value[block_offset + offset] = f(gi, gj);
} else {
mat->value[block_offset + offset] = 0.0;
}
}
}
}
}
}
void dist_matrix_print(struct dbcl_t *mat) {
int rank, size;
MPI_Comm_rank(mat->comm, &rank);
MPI_Comm_size(mat->comm, &size);
double *global_mat;
if (rank == ROOT) {
global_mat = malloc(sizeof(double) * (mat->m * mat->n));
if (global_mat == NULL)
exitWithError("dist_matrix_print: malloc failed( global_mat )\n");
}
int send_size = (mat->lM * mat->lN) * (mat->bm * mat->bn);
int recv_size = send_size;
MPI_Gather(mat->value, send_size, MPI_DOUBLE, global_mat, recv_size, MPI_DOUBLE, ROOT, mat->comm);
if (rank == ROOT) {
printf("Print Matrix >>> (m, n): %d %d (lM, lN): %d %d (bm, bn): %d %d (p, q): %d %d\n", mat->m, mat->n, mat->lM, mat->lN, mat->bm, mat->bn, mat->p, mat->q);
int colors[] = {31, 32, 33, 34, 35, 36, 37, 90, 91, 92, 93, 94, 95, 96};
int background[] = {003, 007};
int gi, gj;
for (gi=0; gi<mat->m; gi++ ) {
for (gj=0; gj<mat->n; gj++ ) {
int i_rank = (gi / mat->bm) % mat->p + ((gj / mat->bn) % mat->q) * mat->p;
int proc_offset = i_rank * (mat->lM * mat->lN) * (mat->bm * mat->bn);
int lbi = gi / (mat->bm * mat->p);
int lbj = gj / (mat->bn * mat->q);
int block_offset = (lbi + lbj * mat->lM) * (mat->bm * mat->bn);
int i = gi % mat->bm;
int j = gj % mat->bn;
int index_offset = i + (j * mat->bm);
char format_buffer[16];
sprintf(format_buffer, "\033[%d;%dm", background[(lbi + lbj) % 2], colors[i_rank % 14]);
printf("%s%2.1f\033[0m ", format_buffer, global_mat[proc_offset + block_offset + index_offset]);
}
printf("\n");
}
printf("\n");
free(global_mat);
}
MPI_Barrier(mat->comm);
}
void ofstrOpen (std::string fileName, std::string errorID, Parameters *P, ofstream & ofStream) {//open file 'fileName', generate error if cannot open
ofStream.open(fileName.c_str(), std::fstream::out | std::fstream::trunc);
if (ofStream.fail()) {//
// dir1=fileName.substr(0,fileName.find_last_of("/")+1);
// if (dir1=="") dir1="./";
ostringstream errOut;
errOut << errorID<<": exiting because of *OUTPUT FILE* error: could not create output file "<< fileName <<"\n";
errOut << "Solution: check that the path exists and you have write permission for this file\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_FILE_OPEN, *P);
};
};
void Genome::HandleSharedMemoryException(const SharedMemoryException & exc, uint64 shmSize)
{
ostringstream errOut;
errOut << "Shared memory error: " << exc.GetErrorCode() << ", errno: " << strerror(exc.GetErrorDetail()) << "(" << errno << ")" << endl;
int exitCode = EXIT_CODE_SHM;
switch (exc.GetErrorCode())
{
case EOPENFAILED:
errOut << "EXITING because of FATAL ERROR: problems with shared memory: error from shmget() or shm_open()." << endl << flush;
errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory" << endl << flush;
break;
case EEXISTS:
errOut << "EXITING: fatal error from shmget() trying to allocate shared memory piece." << endl;
errOut << "Possible cause 1: not enough RAM. Check if you have enough RAM of at least " << shmSize+2000000000 << " bytes" << endl;
errOut << "Possible cause 2: not enough virtual memory allowed with ulimit. SOLUTION: run ulimit -v " << shmSize+2000000000 << endl;
errOut << "Possible cause 3: allowed shared memory size is not large enough. SOLUTIONS: (i) consult STAR manual on how to increase shared memory allocation; " \
"(ii) ask your system administrator to increase shared memory allocation; (iii) run STAR with --genomeLoad NoSharedMemory" << endl<<flush;
break;
case EFTRUNCATE:
errOut << "EXITING: fatal error from ftruncate() error shared memory." << endl;
errOut << "Possible cause 1: not enough RAM. Check if you have enough RAM of at least " << shmSize+2000000000 << " bytes" << endl << flush;
exitCode = EXIT_CODE_MEMORY_ALLOCATION;
break;
case EMAPFAILED:
errOut << "EXITING because of FATAL ERROR: problems with shared memory: error from shmat() while trying to get address of the shared memory piece." << endl << flush;
errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory" << endl << flush;
break;
case ECLOSE:
errOut << "EXITING because of FATAL ERROR: could not close the shared memory object." << endl << flush;
break;
case EUNLINK:
#ifdef POSIX_SHARED_MEM
errOut << "EXITING because of FATAL ERROR: could not delete the shared object." << endl << flush;
#else
errOut << "EXITING because of FATAL ERROR: problems with shared memory: error from shmctl() while trying to remove shared memory piece." << endl << flush;
errOut << "SOLUTION: check shared memory settings as explained in STAR manual, OR run STAR with --genomeLoad NoSharedMemory to avoid using shared memory" << endl << flush;
#endif
break;
default:
errOut << "EXITING because of FATAL ERROR: There was an issue with the shared memory allocation. Try running STAR with --genomeLoad NoSharedMemory to avoid using shared memory.";
break;
}
try
{
if (sharedMemory != NULL)
sharedMemory->Clean();
}
catch(...)
{}
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, exitCode, *P);
};
void BAMbinSortByCoordinate(uint32 iBin, uint binN, uint binS, uint nThreads, string dirBAMsort, Parameters *P) {
if (binS==0) return; //nothing to do for empty bins
//allocate arrays
char *bamIn=new char[binS];
uint *startPos=new uint[binN*3];
uint bamInBytes=0;
//load all aligns
for (uint it=0; it<nThreads; it++) {
string bamInFile=dirBAMsort+to_string(it)+"/"+to_string((uint) iBin);
ifstream bamInStream (bamInFile.c_str());
bamInStream.read(bamIn+bamInBytes,binS);//read the whole file
bamInBytes += bamInStream.gcount();
bamInStream.close();
remove(bamInFile.c_str());
};
if (bamInBytes!=binS) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the actual size on disk: ";
errOut << binS <<" "<< bamInBytes <<" "<< iBin <<"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, 1, *P);
};
//extract coordinates
for (uint ib=0,ia=0;ia<binN;ia++) {
uint32 *bamIn32=(uint32*) (bamIn+ib);
startPos[ia*3] =( ((uint) bamIn32[1]) << 32) | ( (uint)bamIn32[2] );
startPos[ia*3+2]=ib;
ib+=bamIn32[0]+sizeof(uint32);//note that size of the BAM record does not include the size record itself
startPos[ia*3+1]=*( (uint*) (bamIn+ib) ); //read order
ib+=sizeof(uint);
};
//sort
qsort((void*) startPos, binN, sizeof(uint)*3, funCompareUint2);
BGZF *bgzfBin;
bgzfBin=bgzf_open((dirBAMsort+"/b"+to_string((uint) iBin)).c_str(),("w"+to_string((long long) P->outBAMcompression)).c_str());
outBAMwriteHeader(bgzfBin,P->samHeaderSortedCoord,P->chrName,P->chrLength);
//send ordered aligns to bgzf one-by-one
for (uint ia=0;ia<binN;ia++) {
char* ib=bamIn+startPos[ia*3+2];
bgzf_write(bgzfBin,ib, *((uint32*) ib)+sizeof(uint32) );
};
bgzf_flush(bgzfBin);
bgzf_close(bgzfBin);
//release memory
delete [] bamIn;
delete [] startPos;
};
int* prepareDataFile(const char* imagePath)
{
// Create a buffer for the name of the image
char out_name[256];
// Set the name of the image
sprintf(out_name, "%s/out.data", imagePath);
// Create an output file
int* fout = (int*)malloc(sizeof(int));
*fout = open(out_name, O_CREAT | O_RDWR | O_NONBLOCK, 000777);
if (*fout == -1) exitWithError(out_name);
return fout;
}
// Open the camera device as a file
void openDevice(const char* location, int* fd)
{
*fd = open(location, O_RDWR, 0);
if(*fd==1)
{
exitWithError("Open camera failed");
}
else
{
printf("Opened Camera");
}
}
int main(int argc, char *argv[]) {
int *fd = (int*)malloc(sizeof(int)), qual = 0, fps = 0, bufSize = 0;
char *camera;
if(argc != 5) // Check correct number of args
{
char errorMsg[256];
sprintf(errorMsg, "usage: %s cameraDevice JpegQuality fps bufferSize",
argv[0]);
exitWithError(errorMsg);
}
else
{
camera = argv[1]; // camera location
// Image quality
if(atoi(argv[2]) > 0 && atoi(argv[2]) <= 100) qual = atoi(argv[2]);
else exitWithError("Set JpegQuality between 1 and 100 inclusive.");
// frame delay
if(atoi(argv[3]) > 0) fps = atoi(argv[3]);
// list size
if(atoi(argv[4]) > 0) bufSize = atoi(argv[4]);
}
printf("Camera Interface Copyright (C) 2012 Jacob Appleton\n\n");
printf("This program comes with ABSOLUTELY NO WARRANTY;\n");
printf("This is free software, and you are welcome to redistribute it \n");
printf("under certain conditions.\n");
printf("Visit http://www.gnu.org/licenses/gpl.html for more details.\n\n");
*fd = -1;
openDevice(camera, fd);
getCapabilities(fd);
int* imageCaptureType = (int*)malloc(sizeof(int));
*imageCaptureType = V4L2_BUF_TYPE_VIDEO_CAPTURE;
getFrames(1, 1, fd, imageCaptureType, qual, fps, bufSize);
// Turn the stream off - this will turn off the camera's LED light
ioctl(*fd, VIDIOC_STREAMOFF, imageCaptureType);
closeDevice(fd);
free(fd);
free(imageCaptureType);
pthread_exit(NULL);
return 0;
}
int authenticateBank(Switch *switchTrans, BankAuthorizer *user) {
printf("Usuario: %ld\n", user->id);
printf("Password: %s\n", user->password);
char buffer[BUFF_DEFAULT_SIZE];
if (write(switchTrans->fd, "authbanco", 16) < 0) {
exitWithError();
}
if (read(switchTrans->fd, buffer, BUFF_DEFAULT_SIZE) < 0) {
exitWithError();
}
sprintf(buffer, "%ld", user->id);
if (write(switchTrans->fd, buffer, strlen(buffer) + 1) < 0) {
exitWithError();
}
if (read(switchTrans->fd, buffer, BUFF_DEFAULT_SIZE) < 0) {
exitWithError();
}
if (write(switchTrans->fd, user->password, strlen(user->password) + 1)
< 0) {
exitWithError();
}
if (read(switchTrans->fd, buffer, BUFF_DEFAULT_SIZE) < 0) {
exitWithError();
}
return atoi(buffer);
}
void ifstrOpen (std::string fileName, std::string errorID, std::string solutionString, Parameters *P, ifstream & ifStream) {
//open file 'fileName', generate error if cannot open
ifStream.open(fileName.c_str());
if (ifStream.fail()) {//
ostringstream errOut;
errOut << errorID<<": exiting because of *INPUT FILE* error: could not open input file "<< fileName <<"\n";
errOut << "Solution: check that the file exists and you have read permission for this file\n";
if (solutionString.size()>0) {
errOut << " "<< solutionString <<"\n";
};
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_FILE_OPEN, *P);
};
};
void processTransactions() {
int sockopt = 1;
int fd, fd2; /* los ficheros descriptores */
struct sockaddr_in server;
/* para la información de la dirección del servidor */
struct sockaddr_in client;
/* para la información de la dirección del cliente */
socklen_t sin_size;
/* A continuación la llamada a socket() */
if ((fd = socket(AF_INET, SOCK_STREAM, 0)) == -1) {
exitWithError();
}
server.sin_family = AF_INET;
server.sin_port = htons(DEFAULT_BANK_PORT);
server.sin_addr.s_addr = INADDR_ANY;
/* INADDR_ANY coloca nuestra dirección IP automáticamente */
bzero(&(server.sin_zero), 8);
/* escribimos ceros en el reto de la estructura */
if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &sockopt, sizeof(int)) == -1) {
exitWithError();
}
/* A continuación la llamada a bind() */
if (bind(fd, (struct sockaddr*) &server, sizeof(struct sockaddr)) == -1) {
exitWithError();
}
if (listen(fd, 5) == -1) { /* llamada a listen() */
exitWithError();
}
if (signal(SIGINT, intHandler) == SIG_ERR) {
exitWithError();
}
while (keepRunning) {
sin_size = sizeof(struct sockaddr_in);
/* A continuación la llamada a accept() */
if ((fd2 = accept(fd, (struct sockaddr *) &client, &sin_size)) == -1) {
exitWithError();
}
hablar(fd2);
close(fd2); /* cierra fd2 */
}
printf("deslogeandose\n");
}
// Get a frame from the camera device
void getFrames(int noFrames, int minNoFrames, int* fd, int* imgCaptureType,
int cqual, int fps, int bufferSize)
{
struct v4l2_buffer buf;
struct buffer* bufs;
struct v4l2_requestbuffers reqbuf = getReqBufs(noFrames, minNoFrames, fd);
unsigned int n_buffers, i, ctr = 0;
bool started = FALSE, streamOn = false;
struct lstnode* cNode = allocate(bufferSize);
pthread_mutex_t* mutex = (pthread_mutex_t*)malloc(sizeof(pthread_mutex_t));
pthread_mutex_init(mutex, NULL);
struct imgDetails det = getFrameFormat(fd); // get video format details
bufs = (struct buffer*)calloc(reqbuf.count, sizeof(*bufs)); // alloc buffers
// If allocation fails
if (bufs == NULL) exitWithError("Could not allocate buffers.");
// Map the memory in kernel space to user space to access video efficiently
for (n_buffers = 0; n_buffers < reqbuf.count; n_buffers++)
{
mapBuffer(reqbuf, n_buffers, buf, bufs, fd);
}
// Queue the request struct to v4l2 to retrieve the video data mem location
for(i = 0; i < reqbuf.count; i++) queueBuffer(i, buf, fd);
streamOn = turnOnCamera(fd, streamOn, imgCaptureType); // turn on camera
while(true) //forever
{
if(!started) // if the write data thread has not yet been started
{
started = TRUE;
createThread(cNode, mutex);
}
for(i = 0; i < reqbuf.count; i++) // for each frame returned
{
usleep(fps); // maintain steady frame rate
pthread_mutex_lock(mutex); // lock pointers
createImage(buf, bufs, i, cNode, fd, det, cqual);
cNode = cNode->next; // work with the next node in the list
printf("|%d|\n", ctr++);
pthread_mutex_unlock(mutex); // release locks
queueBuffer(i, buf, fd); // queue up a new buffer
}
}
for (i = 0; i < reqbuf.count; ++i) // unmap memory
{
munmap(bufs[i].start, bufs[i].length);
}
free(mutex);
free(cNode);
free(bufs);
}
void sjdbLoadFromFiles(Parameters *P, SjdbClass &sjdbLoci) {
if (P->sjdbFileChrStartEnd.at(0)!="-") {
for (uint ifile=0;ifile<P->sjdbFileChrStartEnd.size(); ifile++) {
ifstream sjdbStreamIn ( P->sjdbFileChrStartEnd.at(ifile).c_str() );
if (sjdbStreamIn.fail()) {
ostringstream errOut;
errOut << "FATAL INPUT error, could not open input file sjdbFileChrStartEnd=" << P->sjdbFileChrStartEnd.at(ifile) <<"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
sjdbLoadFromStream(sjdbStreamIn, sjdbLoci);
P->inOut->logMain << "Loaded database junctions from file: " << P->sjdbFileChrStartEnd.at(ifile) <<", total number of junctions: "<<sjdbLoci.chr.size()<<" junctions\n\n";
};
}; //if (P->sjdbFileChrStartEnd!="-")
};
void sjdbInsertJunctions(Parameters *P, Genome &genome) {
SjdbClass sjdbLoci;
time_t rawtime;
//load 1st pass junctions
if (P->twoPass.pass1sjFile.size()>0)
{
ifstream sjdbStreamIn ( P->twoPass.pass1sjFile.c_str() );
if (sjdbStreamIn.fail()) {
ostringstream errOut;
errOut << "FATAL INPUT error, could not open input file with junctions from the 1st pass="******"\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
sjdbLoadFromStream(sjdbStreamIn, sjdbLoci);
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the 1st pass file: " << P->twoPass.pass1sjFile <<": "<<sjdbLoci.chr.size()<<" total junctions\n\n";
};
//load from junction files
if (P->sjdbFileChrStartEnd.at(0)!="-")
{
sjdbLoadFromFiles(P,sjdbLoci);
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the sjdbFileChrStartEnd file(s), " << sjdbLoci.chr.size()<<" total junctions\n\n";
};
//load from GTF
if (P->sjdbGTFfile!="-")
{
loadGTF(sjdbLoci, P, P->genomeDirOut);
P->inOut->logMain << timeMonthDayTime(rawtime) << " Loaded database junctions from the GTF file: " << P->sjdbGTFfile<<": "<<sjdbLoci.chr.size()<<" total junctions\n\n";
};
sjdbPrepare (sjdbLoci, P, genome.G, P->nGenome, P->twoPass.dir);//P->nGenome - change when replacing junctions
time ( &rawtime );
P->inOut->logMain << timeMonthDayTime(rawtime) << " Finished preparing junctions" <<endl;
//insert junctions into the genome and SA and SAi
sjdbBuildIndex (P, genome.G, genome.SA, genome.SA2, genome.SAi);
time ( &rawtime );
*P->inOut->logStdOut << timeMonthDayTime(rawtime) << " ..... Finished inserting 1st pass junctions into genome" <<endl;
//re-calculate genome-related parameters
P->winBinN = P->nGenome/(1LLU << P->winBinNbits)+1;
};
int main(int argc, char *argv[]) {
if(argc != 3)
{
exitWithError("Usage: tstream2jpeg data_file_path outputPath");
}
char* tStreamPath = argv[1]; // Set the file in path
char jpegPath[255]; // Buffer for current working dir
int i = 0, len, ctr = 0;
char* workingDir = argv[2];
//getcwd(workingDir, 255); // Get current working directory
FILE* tstream = fopen(tStreamPath, "rb"); // Open the telemetry stream
fseek(tstream, 0, SEEK_END); // Seek to EOF
len = ftell(tstream); // Find file size
fseek(tstream, 0, SEEK_SET); // Seek to beginning of file
byte* buf = (byte*)malloc(len); // Allocate file in memory
fread(buf, 1, len-1, tstream); // Read file into memory
sprintf(jpegPath, "%s/image%d.jpeg", workingDir, i++);
FILE* jpeg = fopen(jpegPath, "wb");
while(ctr < len) // While not at end of buffer
{
ctr++; // Ignore first 0xAA
ctr += 2; // Ignore bytes received
byte conBytes[2]; // Buffer for bytes contained
conBytes[1] = *(buf+(ctr++)); // Fill buffer
conBytes[0] = *(buf+(ctr++)); // Fill buffer
uint16_t con = byteToInt(conBytes); // Get int of bytes contained
printf("Creating image of size %d bytes\n", con);
if(*(buf+ctr) == 0xFF && *(buf+ctr+1) == 0xD8)
{
fclose(jpeg);
sprintf(jpegPath, "%s/image%d.jpeg", workingDir, i++);
jpeg = fopen(jpegPath, "wb");
} // Open JPEG for writing
fwrite(buf+ctr, 1, con, jpeg); // Write to the JPEG
ctr += con; // Move ptr past image data
ctr++; // Ignore checksum
}
free(buf);
fclose(tstream);
return EXIT_SUCCESS;
}
float checkBalance(CreditCard *creditCard) {
FILE *fp;
char buffer[BUFF_DEFAULT_SIZE];
char path[BUFF_DEFAULT_SIZE];
sprintf(path, "./%s",
creditCard->number);
if ((fp = fopen(path, "r")) == NULL) {
//exitWithError();
return -1;
}
if (fgets(buffer, BUFF_DEFAULT_SIZE, fp) < 0) {
exitWithError();
}
char *s = strtok(buffer, ":\n");
s = strtok(NULL, ":\n");
s = strtok(NULL, ":\n");
return atof(s);
}
void ReadAlignChunk::chunkFstreamOpen(string filePrefix, int iChunk, fstream &fstreamOut) {//open fstreams for chunks
ostringstream fNameStream1;
fNameStream1 << filePrefix << iChunk;
string fName1=fNameStream1.str();
P->inOut->logMain << "Opening the file: " << fName1 << " ... " <<flush;
remove(fName1.c_str()); //remove the file
fstreamOut.open(fName1.c_str(),ios::out); //create empty file
fstreamOut.close();
fstreamOut.open(fName1.c_str(), ios::in | ios::out); //re-open the file in in/out mode
if (fstreamOut.fail()) {
P->inOut->logMain << "failed!\n";
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: could not create output file "<< fName1 << "\n";
errOut << "Solution: check that you have permission to write this file\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_INPUT_FILES, *P);
};
P->inOut->logMain << "ok" <<endl;
};
int isValidCreditCard(CreditCard *creditCard) {
char buffer[100];
int read;
FILE *fp;
if ((fp = fopen(
"./accounts.txt",
"r")) == NULL) {
exitWithError();
}
while (fgets(buffer, BUFF_DEFAULT_SIZE, fp) != NULL) {
if (buffer != NULL) {
if (strncmp(creditCard->number, buffer, strlen(creditCard->number))
== 0) {
return isCreditCardAndPassCorrect(buffer, creditCard);
}
}
}
return 0;
}
uint Genome::OpenStream(string name, ifstream & stream)
{
stream.open((P->genomeDir+ "/" +name).c_str(), ios::binary);
if (!stream.good()) {
ostringstream errOut;
errOut << "EXITING because of FATAL ERROR: could not open genome file "<< P->genomeDir << "/" << name <<"\n" << endl;
errOut << "SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions\n" <<flush;
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_GENOME_FILES, *P);
};
uint size = 0;
P->inOut->logMain << "checking " << name << " size";
stream.seekg (0, ios::end);
size=(uint) stream.tellg();
stream.clear();
stream.seekg (0, ios::beg);
P->inOut->logMain << "file size: "<< size <<" bytes; state: good=" <<stream.good()\
<<" eof="<<stream.eof()<<" fail="<<stream.fail()<<" bad="<<stream.bad()<<"\n"<<flush;
return size;
}
void fstreamWriteBig(std::ofstream &S, char* A, unsigned long long N, std::string fileName, std::string errorID, Parameters *P) {
struct statvfs statvfsBuf;
statvfs(fileName.c_str(), &statvfsBuf);
P->inOut->logMain << "Writing " << N << " bytes into " <<fileName << " ; empty space on disk = " << statvfsBuf.f_bavail * statvfsBuf.f_bsize <<" bytes ..." <<flush;
unsigned long long C=0;
unsigned long long iC;
for (iC=0; iC<N/fstream_Chunk_Max; iC++) {
S.write(A+C,fstream_Chunk_Max);
C+=fstream_Chunk_Max;
};
if (!S.fail()) S.write(A+C,N%fstream_Chunk_Max);
if (S.fail()) {//failed to write
struct statvfs statvfsBuf;
statvfs(fileName.c_str(), &statvfsBuf);
// system(( "ls -lL "+ P->genomeDir + " > "+ P->genomeDir +"/error.info 2>&1").c_str());
// ifstream error_info((P->genomeDir +"/error.info").c_str());
// P->inOut->logMain <<error_info.rdbuf();
struct stat statBuf;
stat(fileName.c_str(), &statBuf);
remove(fileName.c_str());
ostringstream errOut;
errOut << errorID<<": exiting because of *OUTPUT FILE* error: could not write the output file "<< fileName <<"\n";
errOut << "fail()=" <<S.fail() <<" ; bad()="<< S.bad()<<"\n";
errOut << "Error while trying to write chunk # " << iC << "; "<< C << " bytes\n";
errOut << "File size full = "<< N <<" bytes\n";
errOut << "File size on disk = " << statBuf.st_size<<" bytes\n";
errOut << "Solution: check that you have enough space on the disk\n";
errOut << "Empty space on disk = " << statvfsBuf.f_bavail * statvfsBuf.f_bsize <<" bytes\n";
exitWithError(errOut.str(),std::cerr, P->inOut->logMain, EXIT_CODE_FILE_WRITE, *P);
};
P->inOut->logMain << " done\n" <<flush;
};
Node *NewickTreeReader::readNode(std::istream &in) const
{
Node *node = new Node();
if(characterStartsBranchNode(peekNextCharacter(in)))
{
ignoreNextCharacter(in);
Node* leftChild = readNode(in);
node->setLfDesc(leftChild);
leftChild->setAnc(node);
if(characterStartsNextChildNode(peekNextCharacter(in)))
{
ignoreNextCharacter(in);
Node* rightChild = readNode(in);
node->setRtDesc(rightChild);
rightChild->setAnc(node);
}
else
{
exitWithError("Tree is not bifurcating.");
}
ignoreNextCharacter(in);
}
node->setName(readName(in));
node->setBrlen(readBranchLength(in));
if (node->getLfDesc() == NULL && node->getRtDesc() == NULL)
{
node->setIsTip(true);
}
return node;
}
