void Genotype::loadList(std::string f)
{
misc.message << "Reading genotypes from files specified in [ " << f << " ]..." << std::endl;
misc.message.tab = " ";
std::ifstream file;
misc.checkFileExists(f);
file.open(f.c_str());
int idx = 0;
std::string line;
while(getline(file,line))
{
std::istringstream sstemp(line);
std::string partialFileName;
sstemp >> partialFileName;
if( idx == 0 )
{
this->load(partialFileName);
}
else
{
misc.setGetElapsedTime("AddGenotype");
misc.message << "Adding genotype..." << std::endl;
Genotype partialGenotype = Genotype(partialFileName);
appendGenotype(&partialGenotype);
misc.message << "Adding genotype needed " << misc.setGetElapsedTime("AddGenotype", true) << std::endl;
}
idx++;
}
file.close();
misc.message.tab = "";
misc.message << "Reading genotype files ended." << std::endl;
}
void Caller::call_node_pileup(const NodePileup& pileup) {
_node = _graph->get_node(pileup.node_id());
assert(_node != NULL);
_node_calls.clear();
char def_char = _leave_uncalled ? '.' : '-';
_node_calls.assign(_node->sequence().length(), Genotype(def_char, def_char));
// todo: parallelize this loop
// process each base in pileup individually
for (int i = 0; i < pileup.base_pileup_size(); ++i) {
if (pileup.base_pileup(i).num_bases() >= _min_depth &&
pileup.base_pileup(i).num_bases() <= _max_depth) {
call_base_pileup(pileup, i);
}
}
// add nodes and edges created when making calls to the output graph
// (_side_map gets updated)
create_node_calls(pileup);
_visited_nodes.insert(_node->id());
}
