void log_write_rec(LOG_REC *log, const char *str, int level)
{
char *colorstr;
struct tm *tm;
time_t now;
int hour, day;
g_return_if_fail(log != NULL);
g_return_if_fail(str != NULL);
if (log->handle == -1)
return;
now = time(NULL);
tm = localtime(&now);
hour = tm->tm_hour;
day = tm->tm_mday;
tm = localtime(&log->last);
day -= tm->tm_mday; /* tm breaks in log_rotate_check() .. */
if (tm->tm_hour != hour) {
/* hour changed, check if we need to rotate log file */
log_rotate_check(log);
}
if (day != 0) {
/* day changed */
log_write_timestamp(log->handle,
settings_get_str("log_day_changed"),
"\n", now);
}
log->last = now;
if (log->colorizer == NULL)
colorstr = NULL;
else
str = colorstr = log->colorizer(str);
if ((level & MSGLEVEL_LASTLOG) == 0)
log_write_timestamp(log->handle, log_timestamp, str, now);
else
write_buffer(log->handle, str, strlen(str));
write_buffer(log->handle, "\n", 1);
signal_emit("log written", 2, log, str);
g_free_not_null(colorstr);
}
int log_start_logging(LOG_REC *log)
{
char *dir;
g_return_val_if_fail(log != NULL, FALSE);
if (log->handle != -1)
return TRUE;
/* Append/create log file */
g_free_not_null(log->real_fname);
log->real_fname = log_filename(log);
if (log->real_fname != NULL &&
strcmp(log->real_fname, log->fname) != 0) {
/* path may contain variables (%time, $vars),
make sure the directory is created */
dir = g_dirname(log->real_fname);
mkpath(dir, log_dir_create_mode);
g_free(dir);
}
log->handle = log->real_fname == NULL ? -1 :
open(log->real_fname, O_WRONLY | O_APPEND | O_CREAT,
log_file_create_mode);
if (log->handle == -1) {
signal_emit("log create failed", 1, log);
log->failed = TRUE;
return FALSE;
}
#ifdef HAVE_FCNTL
memset(&lock, 0, sizeof(lock));
lock.l_type = F_WRLCK;
if (fcntl(log->handle, F_SETLK, &lock) == -1 && errno == EACCES) {
close(log->handle);
log->handle = -1;
signal_emit("log locked", 1, log);
log->failed = TRUE;
return FALSE;
}
#endif
lseek(log->handle, 0, SEEK_END);
log->opened = log->last = time(NULL);
log_write_timestamp(log->handle,
settings_get_str("log_open_string"),
"\n", log->last);
signal_emit("log started", 1, log);
log->failed = FALSE;
return TRUE;
}
int main( int argc, char ** argv){
log_and_screen_printf("Demultiplexer\n\n");
log_and_screen_printf(SVN_VERSION);
log_and_screen_printf(SVN_COMMIT_DATE);
log_and_screen_printf("Compiled on %s at %s \n\n", __DATE__, __TIME__);
if (argc < 2) {
print_help();
}
log_write_timestamp(1);
if (argc == 0) {
print_help();
}
DemultiplexerCmdLine cmd = parse_args(argc, argv);
FILE * in = stdin;
if (cmd.input_reads != NULL) {
in = fopen(cmd.input_reads, "r");
if(in == NULL){
log_and_screen_printf("Unable to open file %s\n", cmd.input_reads);
exit(-1);
}
}
Sequence * seq = sequence_new(cmd.max_read_length, cmd.max_name_length, 33);
seq->header = new_sequence_header(CASAVA_1_8);
header_function * f = (header_function *) seq->header;
char * index = f->get_index(seq);
size_t prefix_length = strlen(cmd.output_folder);
char * output_file = calloc(prefix_length + MAX_FIELD_SIZE + 1, sizeof(char *));
char * index_pointer = output_file + prefix_length;
strcpy(output_file, cmd.output_folder);
printf("prefix: %s\n", output_file);
while (read_sequence_from_fastq(in, seq, cmd.max_read_length)) {
strcpy(index_pointer, index);
// printf("index: %s\n new output: %s\n", index, output_file);
append_sequence(output_file, seq, FASTQ);
}
if (in != stdin) {
fclose(in);
}
return 0;
}
void log_stop_logging(LOG_REC *log)
{
g_return_if_fail(log != NULL);
if (log->handle == -1)
return;
signal_emit("log stopped", 1, log);
log_write_timestamp(log->handle,
settings_get_str("log_close_string"),
"\n", time(NULL));
#ifdef HAVE_FCNTL
memset(&lock, 0, sizeof(lock));
lock.l_type = F_UNLCK;
fcntl(log->handle, F_SETLK, &lock);
#endif
write_buffer_flush();
close(log->handle);
log->handle = -1;
}
