void main(int argc,char **argv){
FILE *fp=fopen(argv[1],"rb");
int quality=read_quality(fp);
quality=set_quality(quality);
printf("q=%d\n",quality);
fclose(fp);
}
Contig
read_contig(const std::string& fasta_filename,
const std::string& quality_filename, const std::string& name)
{
SeqType sequence=read_fasta(fasta_filename,name);
QualSeqType quality=read_quality(quality_filename,name);
return Contig(name,sequence,quality);
}
/* reads from a file data for a sinlge spot, data may be partial */
static
rc_t read_next_spot(const char* blk_pfx, IlluminaFileInfo* file)
{
rc_t rc = 0;
const char* tail = file->line;
if( file->ready ) {
/* data still not used */
return 0;
}
IlluminaFileInfo_init(file);
if( (rc = file_read_line(file, true)) != 0 ) {
return SRALoaderFile_LOG(file->file, klogErr, rc, "$(msg)", "msg=reading more data");
} else if( file->line == NULL ) {
return 0; /* eof */
}
switch( file->type ) {
case eIlluminaNativeFileTypeQSeq:
if( (rc = parse_qseq(file, file->line, file->line_len)) != 0 ) {
return SRALoaderFile_LOG(file->file, klogErr, rc, "$(msg)", "msg=reading qseq");
}
break;
case eIlluminaNativeFileTypeFasta:
case eIlluminaNativeFileTypeNoise:
case eIlluminaNativeFileTypeIntensity:
case eIlluminaNativeFileTypeSignal:
{{
/* read only common first 4 coords into name and prepend with DATA_BLOCK/@name */
if( (rc = read_spot_coord(file, file->line, file->line_len, &tail)) == 0 ) {
if( blk_pfx != NULL ) {
pstring tmp_name;
if( (rc = pstring_copy(&tmp_name, &file->name)) == 0 &&
(rc = pstring_assign(&file->name, blk_pfx, strlen(blk_pfx))) == 0 &&
(rc = pstring_append(&file->name, ":", 1)) == 0 ) {
rc = pstring_concat(&file->name, &tmp_name);
}
}
}
if( rc != 0 ) {
return SRALoaderFile_LOG(file->file, klogErr, rc, "$(msg)", "msg=reading spot coord");
}
break;
}}
case eIlluminaNativeFileTypeQuality4:
if( (rc = read_quality(file->line, file->line_len, &file->read)) != 0 ) {
return SRALoaderFile_LOG(file->file, klogErr, rc, "$(msg)", "msg=reading quality");
} else if( (rc = pstring_assign(&file->name, blk_pfx, strlen(blk_pfx))) != 0 ) {
return SRALoaderFile_LOG(file->file, klogErr, rc, "$(msg)", "msg=name for quality 4");
}
break;
default:
rc = RC(rcSRA, rcFormatter, rcReading, rcFileFormat, rcUnknown);
return SRALoaderFile_LOG(file->file, klogErr, rc, "$(msg)", "msg=processing data line");
break;
}
/* process tail (after coords) for some file types */
file->line_len -= tail - file->line; /* length of tail */
switch( file->type ) {
case eIlluminaNativeFileTypeQSeq:
case eIlluminaNativeFileTypeQuality4:
default:
/* completely processed before */
break;
case eIlluminaNativeFileTypeFasta:
if( (rc = pstring_assign(&file->read.seq, tail, file->line_len)) != 0 ||
!pstring_is_fasta(&file->read.seq) ) {
rc = RC(rcSRA, rcFormatter, rcReading, rcData, rcCorrupt);
return SRALoaderFile_LOG(file->file, klogErr, rc, "$(msg)", "msg=reading fasta");
}
break;
case eIlluminaNativeFileTypeNoise:
if( (rc = read_signal(tail, file->line_len, &file->read.noise)) != 0 ) {
return SRALoaderFile_LOG(file->file, klogErr, rc, "$(msg)", "msg=converting noise");
}
break;
case eIlluminaNativeFileTypeIntensity:
if( (rc = read_signal(tail, file->line_len, &file->read.intensity)) != 0 ) {
return SRALoaderFile_LOG(file->file, klogErr, rc, "$(msg)", "msg=converting intensity");
}
break;
case eIlluminaNativeFileTypeSignal:
if( (rc = read_signal(tail, file->line_len, &file->read.signal)) != 0 ) {
return SRALoaderFile_LOG(file->file, klogErr, rc, "$(msg)", "msg=converting signal");
}
break;
}
file->line = NULL;
file->ready = true;
#if _DEBUGGING
DEBUG_MSG(3, ("name:'%s' [%li:%li:%li:%li]\n", file->name.data,
file->coord[0], file->coord[1], file->coord[2], file->coord[3]));
if( file->read.seq.len ) {
DEBUG_MSG(3, ("seq:'%.*s'\n", file->read.seq.len, file->read.seq.data));
}
if( file->read.qual.len ) {
DEBUG_MSG(3, ("qual{0x%x}: %u bytes\n", file->read.qual_type, file->read.qual.len));
}
#endif
return 0;
}
// Main function
void main(void) {
reset_peripheral(); initClock(); initTimer(); initDisplay(); initPin();
initGPIO(); initADC(); initConsole(); int i = 0;
//init_password();
send_data();
initCircBuf (&speed_buffer, BUF_SIZE); init_set_speed_data(&speed_set_data);
int screen = 0; int screen_prev = 0; float speed = 0; float buffed_speed = 0;
int fake_speed = 0; float acc = 0; float max_acc = 0; //float fuel_eco = 0;
float distance = 0;
bool fix = 0; uint8_t satillite = 0; float quality = 0; clock time;
int aim_pos = 0; unsigned long adc = 0; //int error_stepper = 0;
IntMasterEnable();
while(1){
//reading data
read_data = split_data(UART_char_data_old, read_data); // decode data
speed = read_speed(); //read data into variables
adc = run_adc()/7;
//calculations
aim_pos = speed_feedback(buffed_speed, encoder_1/40, speed_set_data.speed);
if (speed_set_data.enable == 1){
step_motor_control(encoder_1/40, aim_pos);
}
//sending fake data
fake_speed = (int)adc;//= random_at_most(100/1.852);
send_info(fake_speed);//knots
//storing data
store_speed(speed);
buffed_speed = analysis_speed();
acc = read_acceleration(buffed_speed);
max_acc = max_acc_func(acc, max_acc);
time = read_time();
satillite = read_satillite();
fix = read_fix();
quality = read_quality();
debounce_button(); // debounce buttons
screen = read_button_screen(screen, fix);
distance = read_distance();
select_read(); //need a mosfet for turning power off
// select adds a an on and off switch yo
if (screen == 1){
if(screen_prev != 1 && screen == 1){
speed_set_data.speed = buffed_speed;
}
speed_set_data.speed = set_speed(speed_set_data.speed); // set the speed to cruise at
}
if (screen == 2){ //0 to 100
acceleration_test(speed);
}
// refresh chainging
if (fix == 1 && speed_set_data.old == speed_set_data.speed && refresh_rate < 4){
UARTSend((unsigned char *)PMTK_SET_NMEA_UPDATE_5HZ, 18, 0);
refresh_rate += 1;
}
if (i >= 50){
display(screen, buffed_speed, acc, max_acc, speed_set_data.speed, satillite,
encoder_1/40, time, distance, quality, UART_char_data_old, aim_pos, adc, acc_times);
i = 0;
}
screen_prev = screen;
i++;
}
}
