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(); }