+ //run filter on template
+ for (int i = 0; i < templateSeqs.size(); i++) { if (m->control_pressed) { return 0; } runFilter(templateSeqs[i]); }
+
+ string kmerDBNameLeft;
+ string kmerDBNameRight;
+
+ //generate the kmerdb to pass to maligner
+ if (searchMethod == "kmer") {
+ string templatePath = m->hasPath(templateFileName);
+ string rightTemplateFileName = templatePath + "right." + m->getRootName(m->getSimpleName(templateFileName));
+ databaseRight = new KmerDB(rightTemplateFileName, kmerSize);
+
+ string leftTemplateFileName = templatePath + "left." + m->getRootName(m->getSimpleName(templateFileName));
+ databaseLeft = new KmerDB(leftTemplateFileName, kmerSize);
+ #ifdef USE_MPI
+ for (int i = 0; i < templateSeqs.size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ string leftFrag = templateSeqs[i]->getUnaligned();
+ leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
+
+ Sequence leftTemp(templateSeqs[i]->getName(), leftFrag);
+ databaseLeft->addSequence(leftTemp);
+ }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(templateSeqs.size());
+
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ string rightFrag = templateSeqs[i]->getUnaligned();
+ rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
+
+ Sequence rightTemp(templateSeqs[i]->getName(), rightFrag);
+ databaseRight->addSequence(rightTemp);
+ }
+ databaseRight->generateDB();
+ databaseRight->setNumSeqs(templateSeqs.size());
+
+ #else
+ //leftside
+ kmerDBNameLeft = leftTemplateFileName.substr(0,leftTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
+ ifstream kmerFileTestLeft(kmerDBNameLeft.c_str());
+ bool needToGenerateLeft = true;
+
+ if(kmerFileTestLeft){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestLeft, m->getVersion());
+ if (GoodFile) { needToGenerateLeft = false; }
+ }
+
+ if(needToGenerateLeft){
+
+ for (int i = 0; i < templateSeqs.size(); i++) {
+
+ if (m->control_pressed) { return 0; }
+
+ string leftFrag = templateSeqs[i]->getUnaligned();
+ leftFrag = leftFrag.substr(0, int(leftFrag.length() * 0.33));
+
+ Sequence leftTemp(templateSeqs[i]->getName(), leftFrag);
+ databaseLeft->addSequence(leftTemp);
+ }
+ databaseLeft->generateDB();
+
+ }else {
+ databaseLeft->readKmerDB(kmerFileTestLeft);
+ }
+ kmerFileTestLeft.close();
+
+ databaseLeft->setNumSeqs(templateSeqs.size());
+
+ //rightside
+ kmerDBNameRight = rightTemplateFileName.substr(0,rightTemplateFileName.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
+ ifstream kmerFileTestRight(kmerDBNameRight.c_str());
+ bool needToGenerateRight = true;
+
+ if(kmerFileTestRight){
+ bool GoodFile = m->checkReleaseVersion(kmerFileTestRight, m->getVersion());
+ if (GoodFile) { needToGenerateRight = false; }
+ }
+
+ if(needToGenerateRight){
+
+ for (int i = 0; i < templateSeqs.size(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ string rightFrag = templateSeqs[i]->getUnaligned();
+ rightFrag = rightFrag.substr(int(rightFrag.length() * 0.66));
+
+ Sequence rightTemp(templateSeqs[i]->getName(), rightFrag);
+ databaseRight->addSequence(rightTemp);
+ }
+ databaseRight->generateDB();
+
+ }else {
+ databaseRight->readKmerDB(kmerFileTestRight);
+ }
+ kmerFileTestRight.close();
+
+ databaseRight->setNumSeqs(templateSeqs.size());
+ #endif
+ }else if (searchMethod == "blast") {
+
+ //generate blastdb
+ databaseLeft = new BlastDB(-1.0, -1.0, 1, -3);
+
+ for (int i = 0; i < templateSeqs.size(); i++) { databaseLeft->addSequence(*templateSeqs[i]); }
+ databaseLeft->generateDB();
+ databaseLeft->setNumSeqs(templateSeqs.size());
+ }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "doprep");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+vector<Sequence*> ChimeraSlayer::getTemplate(Sequence* q) {
+ try {