// get the libraryID of a record
uint32_t Dedup_LowMem::getLibraryID(SamRecord& record, bool checkTags) {
if ( ( checkTags == false ) && ( numLibraries <= 1 ) ) {
return 0;
} else {
char tag[3];
char vtype;
void* value;
std::string rgID;
record.resetTagIter();
while( record.getNextSamTag(tag,vtype,&value) != false ) {
if ( ( tag[0] == 'R' ) && ( tag[1] == 'G' ) && ( vtype == 'Z' ) ) {
if ( !rgID.empty() ) {
Logger::gLogger->error("Multiple RG tag found in one record. ReadName is %s",record.getReadName());
}
else if ( record.isStringType(vtype) ) {
String s = (String)*(String*)value;
rgID = s.c_str();
}
else {
Logger::gLogger->error("vtype is not string (Z) for RG tag");
}
}
}
if ( rgID.empty() ) {
Logger::gLogger->error("No RG tag is found in read %s",record.getReadName());
return 0;
}
else {
std::map<std::string,uint32_t>::iterator it = rgidLibMap.find(rgID);
if ( it != rgidLibMap.end() ) {
return it->second;
}
else {
Logger::gLogger->warning("RG tag %s does not exist in the header",rgID.c_str());
return 0; // cannot be reached
}
}
}
}
