void Aligner::setMasterDR(std::string& master) {
AL_masterDRToken = mStringCheck->getToken(master);
AL_Offsets[AL_masterDRToken] = (int)(AL_length * CRASS_DEF_CONS_ARRAY_START);
prepareMasterForAlignment(master);
placeReadsInCoverageArray(AL_masterDRToken);
calculateDRZone();
}
void Aligner::setMasterDR(StringToken master) {
AL_masterDRToken = master;
std::string master_string = mStringCheck->getString(AL_masterDRToken);
if (AL_masterDRToken == 0) {
// could not be found, through exception
logError("cannot find the token for DR string "<< master_string);
}
AL_Offsets[AL_masterDRToken] = (int)(AL_length * CRASS_DEF_CONS_ARRAY_START);
prepareMasterForAlignment(master_string);
placeReadsInCoverageArray(AL_masterDRToken);
calculateDRZone();
}