// add a function para new_thres defaults to -1 to later deal with
// reanalysis with higher thres - if statement whether to record base thres
// or new thres (ie if -1, then base)
- save_file << " thres=" << threshold << " >\n";
+ save_file << " thres=" << threshold << " soft_thres=" << soft_thres << " >\n";
path_i = refined_pathz.begin();
paths_end = refined_pathz.end();
data = file_data_line.substr(equal_split_i+1);
threshold = atoi (data.c_str());
file_data_line = file_data_line.substr(space_split_i+1);
-
+ // get cur_threshold
+ //std::cout << "file_data_line: " << file_data_line << "\n";
+ //std::cout << "find(\">\"): " << file_data_line.find(">") << "\n";
+ if (file_data_line.find(">") != 0)
+ {
+ space_split_i = file_data_line.find(" ");
+ header_data = file_data_line.substr(0,space_split_i);
+ equal_split_i = header_data.find("=");
+ data = file_data_line.substr(equal_split_i+1);
+ soft_thres = atoi (data.c_str());
+ file_data_line = file_data_line.substr(space_split_i+1);
+ }
+ else
+ {
+ soft_thres = threshold;
+ }
+ //std::cout << "nway_soft_thres: " << soft_thres << "\n";
//cout << "seq_num=" << species_num << " win=" << win_size;
//cout << " thres=" << threshold << endl;