void InputStructures::DetectFlowOrderzAndKeyFromBam(const SamHeader &samHeader){
//TODO Need to handle multiple BAM files with different flowOrders, at least throw an error for now.
for (BamTools::SamReadGroupConstIterator itr = samHeader.ReadGroups.Begin(); itr != samHeader.ReadGroups.End(); ++itr) {
if (itr->HasFlowOrder()) {
string tmpflowOrder = itr->FlowOrder;
if (bamFlowOrderVector.empty()){
bamFlowOrderVector.push_back(tmpflowOrder);
flowOrder = tmpflowOrder; // first one free
}else { //check if the flowOrder is the same if not throw an error, for now we dont support bams with different flow orders
vector<string>::iterator it = std::find(bamFlowOrderVector.begin(), bamFlowOrderVector.end(), tmpflowOrder);
if (it == bamFlowOrderVector.end()) {
// check to see if flowOrder is a substring/superstring first
std::size_t found_me = std::string::npos; // assume bad
if (tmpflowOrder.length()>flowOrder.length()){
found_me = tmpflowOrder.find(flowOrder);
if (found_me==0){ // must find at first position
flowOrder = tmpflowOrder; // longer superstring
bamFlowOrderVector.push_back(tmpflowOrder);
//cout<< "Super: " << tmpflowOrder.length() << " " << tmpflowOrder << endl;
} else
found_me = std::string::npos;
}else{
found_me = flowOrder.find(tmpflowOrder);
if (found_me==0){ // must find at first position
// substring, so no need to update flowOrder
bamFlowOrderVector.push_back(tmpflowOrder);
//cout << "Sub: " << tmpflowOrder.length() << " "<< tmpflowOrder << endl;
} else
found_me = std::string::npos;
}
if (found_me==std::string::npos){
cerr << "FATAL ERROR: BAM files specified as input have different flow orders. Currently tvc supports only BAM files with same flow order. " << endl;
exit(-1);
}
}
}
flowKey = itr->KeySequence;
}
}
if (bamFlowOrderVector.size()>1)
cout << "Compatibly nested flow orders found: " << bamFlowOrderVector.size() << " using longest, nFlows= " << flowOrder.length() << endl;
//cout << "Final: " << flowOrder.length() << " " << flowOrder << endl;
nFlows = flowOrder.length();
if (nFlows > 0) {
flowSigPresent = true;
treePhaserFlowOrder.SetFlowOrder(flowOrder, nFlows);
key.Set(treePhaserFlowOrder, flowKey, "key");
}
}
void InputStructures::DetectFlowOrderzAndKeyFromBam(const SamHeader &samHeader){
// We only store flow orders that are different from each other in the flow order vector.
// The same flow order but different total numbers of flow map to the same flow order object
// So multiple runs, even with different max flows, point to the same flow order object
// We assume that the read group name is written in the form <run_id>.<Barcode Name>
flow_order_vector.clear();
vector<string> temp_flow_order_vector;
int num_read_groups = 0;
for (BamTools::SamReadGroupConstIterator itr = samHeader.ReadGroups.Begin(); itr != samHeader.ReadGroups.End(); ++itr) {
num_read_groups++;
if (itr->ID.empty()){
cerr << "TVC ERROR: BAM file has a read group without ID." << endl;
exit(EXIT_FAILURE);
}
// We need a flow order to do variant calling so throw an error if there is none.
if (not itr->HasFlowOrder()) {
cerr << "TVC ERROR: read group " << itr->ID << " does not have a flow order." << endl;
exit(EXIT_FAILURE);
}
// Check for duplicate read group ID entries and throw an error if one is found
std::map<string,string>::const_iterator key_it = key_by_read_group.find(itr->ID);
if (key_it != key_by_read_group.end()) {
cerr << "TVC ERROR: Multiple read group entries with ID " << itr->ID << endl;
exit(EXIT_FAILURE);
}
// Store Key Sequence for each read group
// The read group key in the BAM file contains the full prefix: key sequence + barcode + barcode adapter
key_by_read_group[itr->ID] = itr->KeySequence;
// Get run id from read group name: convention <read group name> = <run_id>.<Barcode Name>
string run_id = itr->ID.substr(0,itr->ID.find('.'));
if (run_id.empty()) {
cerr << "TVC ERROR: Unable to extract run id from read group name " << itr->ID << endl;
exit(EXIT_FAILURE);
}
// Check whether an entry already exists for this run id and whether it is compatible
std::map<string,int>::const_iterator fo_it = flow_order_index_by_run_id.find(run_id);
if (fo_it != flow_order_index_by_run_id.end()) {
// Flow order for this run id may be equal or a subset of the stored one
if (temp_flow_order_vector.at(fo_it->second).length() < itr->FlowOrder.length()
or temp_flow_order_vector.at(fo_it->second).substr(0, itr->FlowOrder.length()) != itr->FlowOrder
or num_flows_by_run_id.at(run_id) != (int)(itr->FlowOrder).length())
{
cerr << "TVC ERROR: Flow order information extracted from read group name " << itr->ID
<< " does not match previous entry for run id " << run_id << ": " << endl;
cerr << "Exiting entry : " << temp_flow_order_vector.at(fo_it->second) << endl;
cerr << "Newly extracted: " << itr->FlowOrder << endl;
cerr << temp_flow_order_vector.at(fo_it->second) << endl;
exit(EXIT_FAILURE);
}
// Found matching entry and everything is OK.
continue;
}
// New run id: Check whether this flow order is the same or a sub/ superset of an existing flow order
unsigned int iFO = 0;
for (; iFO< temp_flow_order_vector.size(); iFO++){
// Is the new flow order a subset of an existing flow order?
if ( temp_flow_order_vector.at(iFO).length() >= itr->FlowOrder.length() ) {
if (temp_flow_order_vector.at(iFO).substr(0, itr->FlowOrder.length()) == itr->FlowOrder ) {
flow_order_index_by_run_id[run_id] = iFO;
num_flows_by_run_id[run_id] = itr->FlowOrder.length();
break;
}
else
continue;
}
// Is the new flow order a superset of an existing flow order?
if ( temp_flow_order_vector.at(iFO).length() < itr->FlowOrder.length() ) {
if ( itr->FlowOrder.substr(0, temp_flow_order_vector.at(iFO).length()) == temp_flow_order_vector.at(iFO) ) {
temp_flow_order_vector.at(iFO) = itr->FlowOrder;
flow_order_index_by_run_id[run_id] = iFO;
num_flows_by_run_id[run_id] = itr->FlowOrder.length();
break;
}
}
}
// Do we have a new flow order?
if (iFO == temp_flow_order_vector.size()) {
temp_flow_order_vector.push_back(itr->FlowOrder);
flow_order_index_by_run_id[run_id] = iFO;
num_flows_by_run_id[run_id] = itr->FlowOrder.length();
}
} // --- end loop over read groups
// Now we have amassed all the unique flow orders and can construct the FlowOrder objects
for (unsigned int iFO=0; iFO < temp_flow_order_vector.size(); iFO++){
ion::FlowOrder tempIonFlowOrder(temp_flow_order_vector.at(iFO), temp_flow_order_vector.at(iFO).length());
flow_order_vector.push_back(tempIonFlowOrder);
}
// Verbose output
cout << "TVC found a total of " << flow_order_vector.size() << " different flow orders of max flow lengths: ";
int iFO=0;
for (; iFO<(int)flow_order_vector.size()-1; iFO++)
cout << flow_order_vector.at(iFO).num_flows() << ',';
cout << flow_order_vector.at(iFO).num_flows() << endl;
}