int main(int argc, char** argv){
vector<string> g_files;
bool block_order = false;
if (argc == 1){
cerr << "gfa_sort [-b ] -i <GFA_File> >> my_sorted_gfa.gfa" << endl;
exit(0);
}
int c;
while (true){
static struct option long_options[] =
{
{"help", no_argument, 0, 'h'},
{"block-order", no_argument, 0, 'b'},
{"gfa-file", required_argument, 0, 'i'},
{0,0,0,0}
};
int option_index = 0;
c = getopt_long(argc, argv, "hbi:", long_options, &option_index);
if (c == -1){
break;
}
switch (c){
case 'i':
g_files.push_back( optarg );
break;
case '?':
case 'h':
cerr << "gfa_merge [-b --block-order ] -i <GFA_File> -i <OTHER_GFA_FILE> >> my_sorted_gfa.gfa" << endl;
exit(0);
case 'b':
block_order = true;
break;
default:
abort();
}
}
int last_prev_id = 0;
for (auto gfi : g_files){
GFAKluge gg;
gg.parse_gfa_file(gfi);
// get previous ID
// if it is greater than the minimum ID in this gg,
// increment all IDs in gg by the prev_id.
// output this updated gg
cout << gg.to_string();
}
}
int main(int argc, char** argv){
string gfa_file = "";
bool show_nodes = false;
bool show_edges = false;
bool show_containments = false;
bool show_alignments = false;
bool show_length = false;
if (argc == 1){
cerr << "gfa_stats [ -n -e -s -l ] -i <GFA_File> " << endl;
exit(0);
}
int c;
while (true){
static struct option long_options[] =
{
{"help", no_argument, 0, 'h'},
{"num-nodes", no_argument, 0, 'n'},
{"num-edges", no_argument, 0, 'e'},
{"length", no_argument, 0, 'l'},
{"all", no_argument, 0, 's'},
{"gfa-file", required_argument, 0, 'i'},
{0,0,0,0}
};
int option_index = 0;
c = getopt_long(argc, argv, "hnesli:", long_options, &option_index);
if (c == -1){
break;
}
switch (c){
case 'i':
gfa_file = optarg;
break;
case '?':
case 'h':
cerr << "gfa_stats [ -n -e -s -l ] -i <GFA_File> " << endl;
exit(0);
case 'e':
show_edges = true;
break;
case 'n':
show_nodes = true;
break;
case 's':
show_nodes = true;
show_length = true;
show_edges = true;
default:
abort();
}
}
GFAKluge gg;
gg.parse_gfa_file(gfa_file);
if (show_nodes){
int num_nodes = gg.get_name_to_seq().size();
cout << "Number of nodes: " << num_nodes << endl;
}
if (show_edges){
int num_edges = 0;
map<string, vector<link_ele> >::iterator it;
for (gg.get_seq_to_link().size();
cout << "Number of edges: " << num_edges << endl;
}
if (show_length){
//This one's exciting. Let's iterate over the sequence elements and sum
//the length of their sequence.
map<string, sequence_elem, custom_key> my_seqs = gg.get_name_to_seq();
map<string, sequence_elem, custom_key>::iterator it;
int64_t total_len = 0;
for (it = my_seqs.begin(); it != my_seqs.end(); it++){
total_len += (it->second).sequence.size();
}
cout << "Total graph length in basepairs: " << total_len << endl;
}
return 0;
}