void RecalibrationHandler::ReadRecalibrationFromComments(const SamHeader &samHeader, int max_flows_protect) {
// Read comment lines from Sam header
// this will grab json files
if (samHeader.HasComments()) {
// parse the comment lines
for (unsigned int i_co=0; i_co<samHeader.Comments.size(); i_co++) {
// try printing for now
//cout << samHeader.Comments[i_co] << endl;
// might be all sorts of comments in the file
// therefore must find the unlikely magic code in the line before trying to parse
string magic_code = "6d5b9d29ede5f176a4711d415d769108"; // md5hash "This uniquely identifies json comments for recalibration."
bool valid_line = false;
std::size_t found = samHeader.Comments[i_co].find(magic_code);
if (found !=std::string::npos)
valid_line = true;
if (valid_line) {
// very likely to be a properly formatted json object coming from basecaller
Json::Value recal_params(Json::objectValue);
Json::Reader recal_reader;
bool parse_success = recal_reader.parse(samHeader.Comments[i_co], recal_params);
if (!parse_success) {
cout << "failed to parse comment line" << recal_reader.getFormattedErrorMessages() << endl;
} else {
// you are a recalibration object waiting to happen
// let us parse you
// basic ID
//cout << my_members[0] << endl;
string my_block_key = recal_params["MasterKey"].asCString();
//cout << my_block_key << "\t" << recal_params[my_block_key]["modelParameters"].size() << endl;
recalModel.InitializeFromJSON(recal_params, my_block_key, false,max_flows_protect); // don't spam here
// add a map to this entry
bam_header_recalibration.insert(pair<string,RecalibrationModel>(my_block_key, recalModel));
// parse out important information from the block key
// must look like <runid>.block_X%d_Y%d
int end_runid = my_block_key.find(".");
int bloc_loc = my_block_key.find("block_X")+7;
int y_loc = my_block_key.find("_Y");
// glorified assembly language
string runid = my_block_key.substr(0,end_runid);
int x_coord = atoi(my_block_key.substr(bloc_loc,y_loc-bloc_loc).c_str());
int y_coord = atoi(my_block_key.substr(y_loc+2, my_block_key.size()-y_loc+2).c_str());
//cout << runid << "\t" << x_coord << "\t" << y_coord << endl;
block_hash.insert(pair<string, pair<int,int > >(runid,pair<int,int>(x_coord,y_coord)));
is_live = true; // found at least one recalibration entry
}
}
}
}
// okay, now, avoid spamming with possibly large number of lines
if (is_live){
cout << "Recalibration was detected from comment lines in bam file(s)" << endl;
cout << bam_header_recalibration.size() << " unique blocks of recalibration info detected." << endl;
}
}
void RecalibrationHandler::ReadRecalibrationFromComments(const SamHeader &samHeader, const map<string, int> &max_flows_by_run_id) {
if (not samHeader.HasComments())
return;
unsigned int num_parsing_errors = 0;
// Read comment lines from Sam header
for (unsigned int i_co=0; i_co<samHeader.Comments.size(); i_co++) {
// There might be all sorts of comments in the file
// therefore must find the unlikely magic code in the line before trying to parse
string magic_code = "6d5b9d29ede5f176a4711d415d769108"; // md5hash "This uniquely identifies json comments for recalibration."
if (samHeader.Comments[i_co].find(magic_code) == std::string::npos) {
//cout << endl << "No magic code found in comment line "<< i_co <<endl;
//cout << samHeader.Comments.at(i_co) << endl;
continue;
}
// Parse recalibration Json object
Json::Value recal_params(Json::objectValue);
Json::Reader recal_reader;
if (not recal_reader.parse(samHeader.Comments[i_co], recal_params)) {
cerr << "Failed to parse recalibration comment line " << recal_reader.getFormattedErrorMessages() << endl;
num_parsing_errors++;
continue;
}
string my_block_key = recal_params["MasterKey"].asString();
// Assumes that the MasterKey is written in the format <run_id>.block_X<x_offset>_Y<y_offset>
int end_runid = my_block_key.find(".");
int x_loc = my_block_key.find("block_X")+7;
int y_loc = my_block_key.find("_Y");
// glorified assembly language
string runid = my_block_key.substr(0,end_runid);
int x_coord = atoi(my_block_key.substr(x_loc,y_loc-x_loc).c_str());
int y_coord = atoi(my_block_key.substr(y_loc+2, my_block_key.size()-y_loc+2).c_str());
// Protection against not having a flow order for a specified recalibration run id
std::map<string, int>::const_iterator n_flows = max_flows_by_run_id.find(runid);
if (n_flows == max_flows_by_run_id.end()) {
cerr << "TVC ERROR: Recalibration information found for run id " << runid
<< " but there is no matching read group with this run id in the bam header." << endl;
exit(EXIT_FAILURE);
}
//recalModel.InitializeFromJSON(recal_params, my_block_key, false, max_flows_by_run_id.at(runid));
// void RecalibrationModel::InitializeFromJSON(Json::Value &recal_params, string &my_block_key, bool spam_enabled, int over_flow_protect) {
// The calibration comment line contains info about the hp threshold used during base calling, so set to zero here
// XXX FIXME: The number of flows in the TVC group can be larger than the one specified in the calibration block.
recalModel.InitializeModelFromJson(recal_params, n_flows->second);
bam_header_recalibration.insert(pair<string,LinearCalibrationModel>(my_block_key, recalModel));
block_hash.insert(pair<string, pair<int,int > >(runid,pair<int,int>(x_coord,y_coord)));
is_live = true; // found at least one recalibration entry
}
// Verbose output
if (is_live){
cout << "Recalibration was detected from comment lines in bam file(s):" << endl;
cout << bam_header_recalibration.size() << " unique blocks of recalibration info detected." << endl;
}
if (num_parsing_errors > 0) {
cout << "Failed to parse " << num_parsing_errors << " recalibration comment lines." << endl;
}
}