int
fastq_read_check (char *begin, int length, char model, bloom * bl,
float tole_rate, F_set * File_head)
{
char *p = begin;
int distance = length;
int signal = 0, result = 0;
char *previous, *key = (char *) malloc (bl->k_mer * sizeof (char) + 1);
while (distance > bl->k_mer)
{
if (signal == 1)
break;
if (distance >= bl->k_mer)
{
memcpy (key, p, sizeof (char) * bl->k_mer); //need to be tested
key[bl->k_mer] = '\0';
p += bl->k_mer;
previous = p;
distance -= bl->k_mer;
}
else
{
memcpy (key, previous + distance, sizeof (char) * bl->k_mer);
p += (bl->k_mer - distance);
signal = 1;
}
if (model == 'r')
rev_trans (key);
if (bloom_check (bl, key))
{
result =
fastq_full_check (bl, begin, length, model, tole_rate, File_head);
if (result > 0)
return result;
else if (model == 'n')
break;
}
} //outside while
if (model == 'r')
return 0;
else
return fastq_read_check (begin, length, 'r', bl, tole_rate, File_head);
}
/*cut the reads from the string and process them one by one*/
void read_process (bloom * bl, Queue * info, Queue * tail, F_set * File_head, float sampling_rate, float tole_rate, char mode, char fmt_type)
{
char *start_point = info->location;
char *next_job = NULL, *temp = NULL, *previous_point = NULL, *temp_next = NULL;
int result = 0;
next_job = check_fmt (info, tail, start_point, fmt_type);
// make sure it can handle DOS and Unix format ('\r\n' and '\n')
// XXX: what about OSX sinle '\n' ('a0' in hexa)?
if (next_job == NULL)
return;
while (start_point != next_job)
{
if (mode == 'c')
{
if (sampling_rate<1)
temp = jump (start_point, fmt_type, sampling_rate);
else
temp = start_point;
// function for fast/proportional scan
if (start_point != temp)
{
start_point = temp;
continue;
}
}
// skip to the next read if needed
#pragma omp atomic
File_head->reads_num++;
// atomic process for summing reads number
previous_point = start_point;
start_point = get_right_sp (start_point, fmt_type);
// skip the ID line
if (fmt_type == '@')
{
//identify read as fastq format read and pass it to fastq_read_check to process
result = fastq_read_check (start_point, strchr (start_point, '\n') - start_point, 'n', bl, tole_rate, File_head);
start_point = strchr (start_point, '\n') + 1;
start_point = strchr (start_point, '\n') + 1;
start_point = strchr (start_point, '\n') + 1;
}
else
{
temp_next = strchr(start_point+1,'>');
if (temp_next == NULL)
temp_next = next_job;
//identify read as fasta format read and pass it to fasta_read_check to process
result = fasta_read_check (start_point, temp_next-start_point, 'n', bl, tole_rate, File_head);
start_point = temp_next;
}
if (result>0)
{
#pragma omp atomic
File_head->reads_contam++;
if (mode == 'r')
{
#pragma omp critical
{
memcpy(_contam,previous_point,start_point-previous_point);
_contam+=(start_point-previous_point);
}
}
}
else
{
if (mode == 'r')
{
#pragma omp critical
{
memcpy(_clean,previous_point,start_point-previous_point);
_clean+=(start_point-previous_point);
}
}
}
} // outside while
}
