}
}
- printBlock(chimeraResults[0], out);
+ printBlock(chimeraResults[0], chimeraFlag, out);
out << endl;
}else { out << querySeq->getName() << "\tno" << endl; }
}
}
- outputString = getBlock(chimeraResults[0]);
+ outputString = getBlock(chimeraResults[0], chimeraFlag);
outputString += "\n";
//cout << outputString << endl;
//write to output file
//referenceSeqs, numWanted, matchScore, misMatchPenalty, divR, minSimilarity
maligner = new Maligner(templateSeqs, numWanted, match, misMatch, divR, minSim, minCov, searchMethod, databaseLeft, databaseRight);
slayer = new Slayer(window, increment, minSim, divR, iters, minSNP);
-
+
if (m->control_pressed) { return 0; }
string chimeraFlag = maligner->getResults(query, decalc);
if (m->control_pressed) { return 0; }
vector<results> Results = maligner->getOutput();
-
+
//found in testing realigning only made things worse
if (realign) {
ChimeraReAligner realigner(templateSeqs, match, misMatch);
}
}
//***************************************************************************************************************
-void ChimeraSlayer::printBlock(data_struct data, ostream& out){
+void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
try {
//out << ":)\n";
out << data.divr_qla_qrb << '\t' << data.qla_qrb << '\t' << data.bsa << '\t';
out << data.divr_qlb_qra << '\t' << data.qlb_qra << '\t' << data.bsb << '\t';
- out << "yes\t" << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
+ out << flag << '\t' << spotMap[data.winLStart] << "-" << spotMap[data.winLEnd] << '\t' << spotMap[data.winRStart] << "-" << spotMap[data.winREnd] << '\t';
//out << "Similarity of parents: " << data.ab << endl;
//out << "Similarity of query to parentA: " << data.qa << endl;
}
}
//***************************************************************************************************************
-string ChimeraSlayer::getBlock(data_struct data){
+string ChimeraSlayer::getBlock(data_struct data, string flag){
try {
string outputString = "";
outputString += toString(data.divr_qla_qrb) + "\t" + toString(data.qla_qrb) + "\t" + toString(data.bsa) + "\t";
outputString += toString(data.divr_qlb_qra) + "\t" + toString(data.qlb_qra) + "\t" + toString(data.bsb) + "\t";
- outputString += "yes\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
+ outputString += flag + "\t" + toString(spotMap[data.winLStart]) + "-" + toString(spotMap[data.winLEnd]) + "\t" + toString(spotMap[data.winRStart]) + "-" + toString(spotMap[data.winREnd]) + "\t";
return outputString;
}