void header::reparse()
{
unsigned int index = 0;
has_idx = false; contig_index = 0;
vector<string> old_lines(lines.size(),"");
copy(lines.begin(), lines.end(), old_lines.begin());
lines.resize(0);
INFO_map.clear(); INFO_reverse_map.clear();
FILTER_map.clear(); FILTER_reverse_map.clear();
FORMAT_map.clear(); FORMAT_reverse_map.clear();
CONTIG_map.clear(); CONTIG_reverse_map.clear();
index += add_FILTER_descriptor("ID=PASS,Description=PASS", index);
for (unsigned int ui=0; ui<old_lines.size(); ui++)
parse_meta(old_lines[ui],index);
}
// embed lines within new tag and indent embedded lines two spaces
static void embed_in_tag(std::string tag, std::vector<std::string>& lines) {
std::string open_tag = "<" + tag + ">";
std::string close_tag = "</" + tag + ">";
std::vector<std::string> old_lines(lines);
lines.clear();
// put in open tag
lines.push_back(" " + open_tag);
// put in indented lines
for (std::vector<std::string>::const_iterator it = old_lines.begin(); it != old_lines.end(); ++it) {
lines.push_back(" " + *it);
}
// put in close tag
lines.push_back(" " + close_tag);
}
