std::string Breakpoint::to_string() {
std::stringstream ss;
if (positions.support.size() > 1) {
ss << "\t\tTREE: ";
ss << TRANS_type(this->get_SVtype());
ss << " ";
ss << get_coordinates().start.min_pos;
ss << ":";
ss << get_coordinates().stop.max_pos;
ss << " ";
ss << this->length;
ss << " ";
ss << positions.support.size();
ss << " ";
ss << get_strand(2);
}
return ss.str();
}
std::string BAMUtils::to_string() {
std::ostringstream strm(std::ostringstream::app);
strm << get_name(); //0
strm << "\t";
strm << get_strand(); //1
strm << "\t";
strm << get_t_start(); //2
strm << "\t";
strm << get_t_length(); //3
strm << "\t";
strm << get_q_length();//4
strm << "\t";
strm << get_match();//5
strm << "\t";
strm << get_percent_id();//6
strm << "\t";
strm << get_q_error();//7
strm << "\t";
strm << get_homo_errors();//8
strm << "\t";
strm << get_mismatch_errors();//9
strm << "\t";
strm << get_indel_errors();//10
strm << "\t";
strm << get_qdna();//12
strm << "\t";
strm << get_matcha();//13
strm << "\t";
strm << get_tdna();//14
strm << "\t";
strm << get_rname();//15
strm << "\t";
if (num_slop >= 0) {
strm << num_slop;
}else {
strm << 0;//16
}
strm << "\t";
std::vector<std::string> q_score_vec;
split(q_scores, ',', q_score_vec);
for (std::vector<std::string>::size_type i = 0; i < q_score_vec.size(); i++) {
//strm << phred_lens[i];
strm << get_phred_len((strtol(q_score_vec[i].c_str(),NULL, 10)));
strm << "\t";
}
strm << get_full_q_length();
strm << "\t";
return strm.str();
}
