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();
}
void Aligner::alignSlave(StringToken& slaveDRToken) {
AL_Offsets[slaveDRToken] = -1;
std::string slaveDR = mStringCheck->getString(slaveDRToken);
AlignerFlag_t flags;
int offset = getOffsetAgainstMaster(slaveDR, flags);
if (flags[score_equal]) {
std::string extended_slave_dr;
extendSlaveDR(slaveDR, extended_slave_dr);
flags.reset();
offset = getOffsetAgainstMaster(extended_slave_dr, flags);
if (flags[score_equal]) {
logWarn("Alignment Warning: Extended Slave scores equal",4);
logWarn("\tCannot place slave: "<<slaveDR<<" ("<<slaveDRToken<<") in array", 4);
logWarn("\tOriginal slave: "<<slaveDR, 4);
logWarn("\tExtended Slave: "<<extended_slave_dr, 4);
logWarn("\tMaster: "<<mStringCheck->getString(AL_masterDRToken), 4);
logWarn("******", 4);
flags[failed] = true;
}
}
if (flags[failed]) {
if(! flags[score_equal]){
logWarn("Alignment Warning: Alignment failed", 4);
logWarn("\tCannot place slave: "<<slaveDR<<" ("<<slaveDRToken<<") in array", 4);
logWarn("\tMaster: "<<mStringCheck->getString(AL_masterDRToken), 4);
logWarn("******", 4);
}
return;
}
if (flags[reversed] ) {
// we need to reverse all the reads and the DR for these reads
try {
ReadListIterator read_iter = mReads->at(slaveDRToken)->begin();
while (read_iter != mReads->at(slaveDRToken)->end())
{
(*read_iter)->reverseComplementSeq();
read_iter++;
}
} catch(crispr::exception& e) {
std::cerr<<e.what()<<std::endl;
throw crispr::exception(__FILE__,
__LINE__,
__PRETTY_FUNCTION__,
"cannot reverse complement sequence");
}
// fix the places where the DR is stored
slaveDR = reverseComplement(slaveDR);
StringToken st = mStringCheck->addString(slaveDR);
(*mReads)[st] = (*mReads)[slaveDRToken];
(*mReads)[slaveDRToken] = NULL;
slaveDRToken = st;
}
//std::cerr << AL_Offsets[AL_masterDRToken] + offset <<std::endl;
AL_Offsets[slaveDRToken] = AL_Offsets[AL_masterDRToken] + offset;
placeReadsInCoverageArray(slaveDRToken);
}
