pid_t op_pipe(t_ast *tree, int pfd_old[2])
{
int pfd[2];
pid_t pid;
pid = 0;
if (pipe(pfd) != -1)
{
if (tree->left)
{
if (tree->left->tk->prio == 1)
ft_redir_pipe(tree, pfd_old, pfd);
else
pid = execute(tree->left->tk->value, pfd_old, pfd, 1);
if (pfd_old)
close_pfd(pfd_old);
if (tree->right && tree->right->tk->prio > 0)
resolve_tree(tree->right, pfd);
else
op_pipe2(tree, pfd, &pid);
}
else
error("42sh: parse error near `|'\n");
}
return (pid);
}
void op_pipe3(t_ast *tree, t_token *token, int pfd[2], int *pid)
{
if (token)
fill_tree(token, &tree->right);
if (tree->right && tree->right->tk->prio > 0)
resolve_tree(tree->right, pfd);
else
op_pipe2(tree, pfd, pid);
}
int classify_seq(kseq_t *trunk, int trunkNum, bwt& bt, cly_r *results, int offset)
{
int read_len;
char *useRead;
char *qual;
int match_len;
int matchNum;
//int spacedLen;
int counterIntervals;
int hit_counter;
//fprintf(stderr,"dddddd");
for (int i=0; i<trunkNum; ++i) {
read_len = trunk[i].seq.l;
useRead = trunk[i].seq.s;
qual = trunk[i].qual.s;
map<uint32_t, uint32_t> hit_times;
transIntoBytes(useRead, read_len);
//cout<<useRead<<endl;i
counterIntervals = splitBytes(byteFormat, read_len, _kmer);
//cout<<counterIntervals<<endl;
int spacedLen = 20;
hit_counter = 0;
//int ind = 4;
while (spacedLen) {
//spacedLen = spacedLeng[ind];
for (int j=0; j<counterIntervals;++j) {
int start = intervals[(j<<1)];
int p_len = intervals[(j<<1) + 1];
//cout<<p_len<<"\t"<<start<<endl;
do {
matchNum = bt.exactMatch(byteFormat + start, p_len, match_len, assignedTID);
//cout<<match_len<<"\t"<<mismatch<<endl;
//cout<<match_len<<"\t"<<p_len<<"\t"<<spacedLen<<endl;
//if (matchNum) {
//++hit_counter;
while (matchNum) {
++hit_counter;
hit_times[assignedTID[--matchNum]] += match_len;
//cout<<assignedTID[matchNum]<<"\t";
}
//}
//cout<<endl;
if (match_len < spacedLen) p_len -= spacedLen;
else p_len -= (match_len/spacedLen)*spacedLen;
} while (p_len > _kmer);
}
if (hit_counter)
break;
else
//--ind;
spacedLen -= 5;
}
//cout<<endl;
cly_r *results_bulk = results + (i << 1) + offset;
int buff_pos = 0;
results_bulk->read_Name = trunk[i].name.s;
//hit_times[1286170] = 29;
map<uint32_t, uint32_t>::iterator it = hit_times.begin();
while (buff_pos < 2026 && it != hit_times.end() ) {
//buff_pos += sprintf(results_bulk->algn_r + buff_pos, "%u:%u ", it->first, it->second );
++it;
}
results_bulk->algn_r[buff_pos] = '\0';
//cout<<endl;
uint32_t lab = resolve_tree(hit_times);
if (lab) {
results_bulk->tid = lab;
results_bulk->isClassified = 'C';
} else {
results_bulk->tid = 0;
results_bulk->isClassified = 'U';
}
}
//fprintf(stderr,"seconds %f\n",(float)tk/CLOCKS_PER_SEC);
return NORMAL_EXIT;
}
int classify_seq_2(kseq_t *trunk, int trunkNum, bwt& bt, cly_r *results)
{
int read_len;
char *useRead;
char *qual;
int match_len;
int matchNum;
int counterIntervals;
for (int i=0; i<trunkNum; ++i) {
read_len = trunk[i].seq.l;
useRead = trunk[i].seq.s;
qual = trunk[i].qual.s;
map<uint32_t, uint32_t> hit_times;
transIntoBytes(useRead, read_len);
//cout<<useRead<<endl;i
counterIntervals = splitBytes(byteFormat, read_len, _kmer);
//cout<<counterIntervals<<endl;
for (int j=0; j<counterIntervals;++j) {
int start = intervals[(j<<1)];
int p_len = intervals[(j<<1) + 1];
//cout<<p_len<<"\t"<<start<<endl;
do {
matchNum = bt.exactMatch(byteFormat + start, p_len, match_len, assignedTID);
//cout<<match_len<<"\t"<<mismatch<<endl;
if (matchNum) {
while (matchNum) hit_times[assignedTID[--matchNum]] += match_len;
p_len -= (match_len - _kmer);
} else
p_len -= _interval;
//cout<<match_len<<"\t"<<p_len<<"\t"<<spacedLen<<endl;
} while (p_len > _kmer);
}
//cout<<endl;
cly_r *results_bulk = results + i;
int buff_pos = 0;
results_bulk->read_Name = trunk[i].name.s;
map<uint32_t, uint32_t>::iterator it = hit_times.begin();
while (it != hit_times.end()) {
buff_pos += sprintf(results_bulk->algn_r + buff_pos, "%u:%u ", it->first, it->second );
++it;
}
results_bulk->algn_r[buff_pos] = '\0';
//cout<<endl;
uint32_t lab = resolve_tree(hit_times);
if (lab) {
results_bulk->tid = lab;
results_bulk->isClassified = 'C';
} else {
results_bulk->tid = 0;
results_bulk->isClassified = 'U';
}
}
//fprintf(stderr,"seconds %f\n",(float)tk/CLOCKS_PER_SEC);
return NORMAL_EXIT;
}
