void HotspotReader::MakeHintQueue(const string& hotspot_vcf_filename)
{
// go through the entire vcf to generate the blacklist
ifstream hotspot_vcf;
hotspot_vcf.open(hotspot_vcf_filename.c_str(), ifstream::in);
string bstrand = "BSTRAND";
while (!hotspot_vcf.eof()) {
string line;
getline(hotspot_vcf, line);
if (line[0] != '#') {
// look for the BSTRAND tag
size_t found = line.find(bstrand);
if (found != string::npos) {
// found BSTRAND, look for semicolon delimiter or end of line
long int hint = NO_HINT;
size_t semicolon_pos = line.find(";", found+bstrand.size());
if (semicolon_pos == string::npos)
semicolon_pos = hotspot_vcf.gcount()-1; // impute a semicolon at the end of the line
// look for the code B
size_t b_pos = line.find("B", found+bstrand.size());
// look for the code R
size_t r_pos = line.find("R", found+bstrand.size());
// look for the code F
size_t f_pos = line.find("F", found+bstrand.size());
bool blacklist = false;
if (f_pos < semicolon_pos) {
hint = FWD_BAD_HINT;
}
if (r_pos < semicolon_pos) {
hint = REV_BAD_HINT;
}
if (b_pos < semicolon_pos){
hint = BOTH_BAD_HINT;
}
if ( (f_pos < semicolon_pos) && (r_pos < semicolon_pos)){
hint = BOTH_BAD_HINT;
}
// blacklist this position
if (hint != NO_HINT) {
// #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT [SAMPLE1 .. SAMPLEN]
vector<string> fields = split(line, '\t');
string sequenceName = fields.at(0);
char* end; // dummy variable for strtoll
long int pos = strtoll(fields.at(1).c_str(), &end, 10);
long int chrom_idx = ref_reader_->chr_idx(sequenceName.c_str());
vector<long int> hint_entry (3, NO_HINT);
hint_entry[0] = chrom_idx;
hint_entry[1] = pos-1;
hint_entry[2] = hint;
hint_vec.push_back(hint_entry);
}
}
}
}
// std::cout << "BL size: " << hint_vec.size() << endl;
}
const char *hint_to_name(glui32 hint) {
#define hint_entry(this) switch_entry(stylehint, hint_name, this)
switch(hint) {
hint_entry(Indentation);
hint_entry(ParaIndentation);
hint_entry(Justification);
hint_entry(Size);
hint_entry(Weight);
hint_entry(Oblique);
hint_entry(Proportional);
hint_entry(TextColor);
hint_entry(BackColor);
hint_entry(ReverseColor);
default:
return "WTF";
break;
}
}
