Path_n_count_pair IRKE::inchworm (KmerCounter& kcounter, char direction, kmer_int_type_t kmer, Kmer_visitor& visitor, float min_connectivity) {
// cout << "inchworm" << endl;
Path_n_count_pair entire_path;
unsigned int inchworm_round = 0;
unsigned long num_total_kmers = kcounter.size();
Kmer_visitor eliminator(kcounter.get_kmer_length(), DOUBLE_STRANDED_MODE);
while (true) {
inchworm_round++;
eliminator.clear();
if (inchworm_round > num_total_kmers) {
throw(string ("Error, inchworm rounds have exceeded the number of possible seed kmers"));
}
if (IRKE_COMMON::MONITOR >= 3) {
cerr << endl << "Inchworm round(" << string(1,direction) << "): " << inchworm_round << " searching kmer: " << kmer << endl;
string kmer_str = kcounter.get_kmer_string(kmer);
cerr << kcounter.describe_kmer(kmer_str) << endl;
}
visitor.erase(kmer); // seed kmer must be not visited already.
Kmer_Occurence_Pair kmer_pair(kmer, kcounter.get_kmer_count(kmer));
Path_n_count_pair best_path = inchworm_step(kcounter, direction, kmer_pair, visitor, eliminator, inchworm_round, 0, min_connectivity, MAX_RECURSION);
if (best_path.second > 0) {
// append info to entire path in reverse order, so starts just after seed kmer
vector<kmer_int_type_t>& kmer_list = best_path.first;
unsigned int num_kmers = kmer_list.size();
int first_index = num_kmers - 1;
int last_index = 0;
if (CRAWL) {
last_index = first_index - CRAWL_LENGTH + 1;
if (last_index < 0) {
last_index = 0;
}
}
for (int i = first_index; i >= last_index; i--) {
kmer_int_type_t kmer_extend = kmer_list[i];
entire_path.first.push_back(kmer_extend);
visitor.add(kmer_extend);
entire_path.second += kcounter.get_kmer_count(kmer_extend);
}
kmer = entire_path.first[ entire_path.first.size() -1 ];
}
else {
// no extension possible
break;
}
}
if (IRKE_COMMON::MONITOR >= 3)
cerr << endl;
return(entire_path);
}
Path_n_count_pair IRKE::inchworm(KmerCounter &kcounter,
char direction,
kmer_int_type_t kmer,
Kmer_visitor &visitor,
float min_connectivity)
{
// cout << "inchworm" << endl;
Path_n_count_pair entire_path;
entire_path.second = 0; // init cumulative path coverage
unsigned int inchworm_round = 0;
unsigned long num_total_kmers = kcounter.size();
Kmer_visitor eliminator(kcounter.get_kmer_length(), DOUBLE_STRANDED_MODE);
while (true) {
if (IRKE_COMMON::__DEVEL_rand_fracture) {
// terminate extension with probability of __DEVEL_rand_fracture_prob
float prob_to_fracture = rand() / (float) RAND_MAX;
//cerr << "prob: " << prob_to_fracture << endl;
if (prob_to_fracture <= IRKE_COMMON::__DEVEL_rand_fracture_prob) {
// cerr << "Fracturing at iworm round: " << inchworm_round << " given P: " << prob_to_fracture << endl;
return (entire_path);
}
}
inchworm_round++;
eliminator.clear();
if (inchworm_round > num_total_kmers) {
throw (string("Error, inchworm rounds have exceeded the number of possible seed kmers"));
}
if (IRKE_COMMON::MONITOR >= 3) {
cerr << endl << "Inchworm round(" << string(1, direction) << "): " << inchworm_round << " searching kmer: "
<< kmer << endl;
string kmer_str = kcounter.get_kmer_string(kmer);
cerr << kcounter.describe_kmer(kmer_str) << endl;
}
visitor.erase(kmer); // seed kmer must be not visited already.
Kmer_Occurence_Pair kmer_pair(kmer, kcounter.get_kmer_count(kmer));
Path_n_count_pair best_path = inchworm_step(kcounter,
direction,
kmer_pair,
visitor,
eliminator,
inchworm_round,
0,
min_connectivity,
MAX_RECURSION);
vector<kmer_int_type_t> &kmer_list = best_path.first;
unsigned int num_kmers = kmer_list.size();
if ((IRKE_COMMON::__DEVEL_zero_kmer_on_use && num_kmers >= 1) || best_path.second > 0) {
// append info to entire path in reverse order, so starts just after seed kmer
int first_index = num_kmers - 1;
int last_index = 0;
if (CRAWL) {
last_index = first_index - CRAWL_LENGTH + 1;
if (last_index < 0) {
last_index = 0;
}
}
for (int i = first_index; i >= last_index; i--) {
kmer_int_type_t kmer_extend = kmer_list[i];
entire_path.first.push_back(kmer_extend);
visitor.add(kmer_extend);
//entire_path.second += kcounter.get_kmer_count(kmer_extend);
// selected here, zero out:
if (IRKE_COMMON::__DEVEL_zero_kmer_on_use) {
kcounter.clear_kmer(kmer_extend);
}
}
kmer = entire_path.first[entire_path.first.size() - 1];
entire_path.second += best_path.second;
}
else {
// no extension possible
break;
}
}
if (IRKE_COMMON::MONITOR >= 3)
cerr << "No extension possible." << endl << endl;
return (entire_path);
}
