/*-------------------------------------*/
int
fasta_read_check (char *begin, char *next, char model, bloom * bl, float tole_rate, F_set * File_head)
{
char *p = strchr (begin + 1, '\n') + 1;
if (!p || *p == '>')
return 1;
int n, m, result, count_enter;
char *key = (char *) malloc ((bl->k_mer + 1) * sizeof (char));
char *pre_key = (char *) malloc ((bl->k_mer + 1) * sizeof (char));
key[bl->k_mer] = '\0';
while (p != next)
{
while (n < bl->k_mer)
{
if (p[m] == '>' || p[m] == '\0')
{
m--;
break;
}
if (p[m] != '\r' && p[m] != '\n')
key[n++] = p[m];
else
count_enter++;
m++;
} //inner while
if (m == 0)
break;
if (strlen (key) == bl->k_mer)
memcpy (pre_key, key, sizeof (char) * (bl->k_mer + 1));
else
{
char *temp_key = (char *) malloc (bl->k_mer * sizeof (char));
memcpy (temp_key, pre_key + strlen (key), bl->k_mer - strlen (key));
memcpy (temp_key + bl->k_mer - strlen (key), key, sizeof (char) * (strlen (key) + 1));
free (key);
key = temp_key;
}
p += m;
n = 0;
m = 0;
if (model == 'r')
rev_trans (key);
if (bloom_check (bl, key))
{
result = fasta_full_check (bl, begin, next, model, tole_rate, File_head);
if (result > 0)
return result;
//else if (model == 'n') //use recursion to check the sequence forward and backward
// return fasta_read_check (begin, next, 'r', bl);
else if (model == 'n')
break;
}
//memset (key, 0, bl->k_mer);
} //outside while
if (model == 'r')
return 0;
else
return fasta_read_check (begin, next, '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
}
