static void
printstate(State *b)
{
if (!b || (!tl_verbose && !b->reachable)) return;
b->reachable = 0; /* print only once */
fprintf(tl_out, "%s:\n", b->name->name);
if (tl_verbose)
{ fprintf(tl_out, " /* ");
dump(b->colors->Other);
fprintf(tl_out, " */\n");
}
if (strncmp(b->name->name, "accept", 6) == 0
&& Max_Red == 0)
fprintf(tl_out, "T0%s:\n", &(b->name->name[6]));
fprintf(tl_out, "\tif\n");
tcnt = 0;
rev_trans(b->trans);
if (!tcnt) fprintf(tl_out, "\t:: false\n");
fprintf(tl_out, "\tfi;\n");
Total++;
}
static void
rev_trans(Transition *t) /* print transitions in reverse order... */
{
if (!t) return;
rev_trans(t->nxt);
if (t->redundant && !tl_verbose) return;
fprintf(tl_out, "\t:: (");
if (dump_cond(t->cond, t->cond, 1))
fprintf(tl_out, "1");
fprintf(tl_out, ") -> goto %s\n", t->name->name);
tcnt++;
}
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);
}
/*-------------------------------------*/
int
fasta_full_check (bloom * bl, char *begin, char *next, char model, float tole_rate, F_set * File_head)
{
int match_s = 0, count = 0, mark = 1;
int n = 0, m = 0, count_enter = 0, match_time = 0;
short previous = 0, conse = 0;
float result;
char *key = (char *) malloc ((bl->k_mer + 1) * sizeof (char));
begin = strchr (begin + 1, '\n') + 1;
char *p = begin;
while (p != next)
{
if (*p == '\n')
count_enter++;
p++;
}
p = begin;
while (*p != '>' && *p != '\0')
{
while (n < bl->k_mer)
{
if (p[m] == '>' || p[m] == '\0')
{
m--;
break;
}
if (p[m] != '\r' && p[m] != '\n')
key[n++] = p[m];
m++;
}
key[n] = '\0';
if (model == 'r')
rev_trans (key);
//printf("key->%s\n",key);
if (count >= bl->k_mer)
{
mark = 1;
count = 0;
}
if (strlen (key) == bl->k_mer)
{
if (bloom_check (bl, key))
{
match_time++;
if (previous == 1)
conse++;
else
{
conse += bl->k_mer;
previous = 1;
}
if (mark == 1)
{
match_s += (bl->k_mer - 1);
mark = 0;
}
else
match_s++;
}
else
{
previous = 0;
//printf("unhit--->\n");
}
count++;
} //outside if
//printf("score->%d\n",match_s);
p++;
if (p[0] == '\n')
p++;
n = 0;
m = 0;
} // end of while
//result = (float) match_s / (float) (next - begin - count_enter);
//result = (float) match_time*(bl->k_mer)/(float)((next-begin-count_enter-bl->k_mer+2)*(bl->k_mer)+2*dx_add(bl->k_mer));
//result = (float) ((match_time+conse)*(bl->k_mer))/(float)((next-begin-count_enter-bl->k_mer+2+conse)*(bl->k_mer)+2*dx_add(bl->k_mer));
//result = (float) ((match_time)*(bl->k_mer))/(float)((next-begin-count_enter-bl->k_mer+2)*(bl->k_mer)+2*dx_add(bl->k_mer));
//result = (float)(match_time*bl->k_mer+conse)/(float)((next-begin-count_enter-bl->k_mer+2)*bl->k_mer+conse+2*dx_add(bl->k_mer));
//printf ("result1->%f\n",result);
//result = (float)(match_time*bl->k_mer)/(float)((next-begin-count_enter)*bl->k_mer-2*dx_add(bl->k_mer-1));
result = (float) (match_time * bl->k_mer + conse) / (float) ((next - begin - count_enter) * bl->k_mer - 2 * bl->dx + (next - begin - count_enter) - bl->k_mer + 1);
#pragma omp atomic
File_head->hits += match_time;
#pragma omp atomic
File_head->all_k += (next - begin - count_enter - bl->k_mer);
if (result >= tole_rate) //match >tole_rate considered as contaminated
return match_s;
else
return 0;
}
/*-------------------------------------*/
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);
}
/*-------------------------------------*/
int
fastq_full_check (bloom * bl, char *p, int distance, char model, float tole_rate, F_set * File_head)
{
//printf ("fastq full check...\n");
int length = distance;
int count = 0, match_s = 0, mark = 1, match_time = 0;
float result;
char *key = (char *) malloc (bl->k_mer * sizeof (char) + 1);
short prev = 0, conse = 0;
while (distance >= bl->k_mer)
{
memcpy (key, p, sizeof (char) * bl->k_mer);
key[bl->k_mer] = '\0';
p += 1;
if (model == 'r')
rev_trans (key);
if (count >= bl->k_mer)
{
mark = 1;
count = 0;
}
if (strlen (key) == bl->k_mer)
{
if (bloom_check (bl, key))
{
match_time++;
if (prev == 1)
conse++;
else
{
conse += bl->k_mer;
prev = 1;
}
if (mark == 1)
{
match_s += (bl->k_mer - 1);
mark = 0;
}
else
match_s++;
}
else
{
prev = 0;
//printf("unhit--->\n");
}
count++;
} //outside if
distance--;
} // end while
free (key);
result = (float) (match_time * bl->k_mer + conse) / (float) (length * bl->k_mer - 2 * bl->dx + length - bl->k_mer + 1);
//result = (float) match_s / (float) length;
#pragma omp atomic
File_head->hits += match_time;
#pragma omp atomic
File_head->all_k += (length - bl->k_mer);
if (result >= tole_rate)
return match_s;
else
return 0;
}
