+ out << flag << '\t' << data.winLStart << "-" << data.winLEnd << '\t' << data.winRStart << "-" << data.winREnd << '\t';
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "printBlock");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+void ChimeraSlayer::printBlock(data_results leftdata, data_results rightdata, bool leftChimeric, bool rightChimeric, string flag, ostream& out){
+ try {
+
+ if ((leftChimeric) && (!rightChimeric)) { //print left
+ out << querySeq.getName() << '\t';
+ out << leftdata.results[0].parentA.getName() << "\t" << leftdata.results[0].parentB.getName() << '\t';
+
+ out << leftdata.results[0].divr_qla_qrb << '\t' << leftdata.results[0].qla_qrb << '\t' << leftdata.results[0].bsa << '\t';
+ out << leftdata.results[0].divr_qlb_qra << '\t' << leftdata.results[0].qlb_qra << '\t' << leftdata.results[0].bsb << '\t';
+
+ out << flag << '\t' << leftdata.results[0].winLStart << "-" << leftdata.results[0].winLEnd << '\t' << leftdata.results[0].winRStart << "-" << leftdata.results[0].winREnd << '\t';
+
+ }else if ((!leftChimeric) && (rightChimeric)) { //print right
+ out << querySeq.getName() << '\t';
+ out << rightdata.results[0].parentA.getName() << "\t" << rightdata.results[0].parentB.getName() << '\t';
+
+ out << rightdata.results[0].divr_qla_qrb << '\t' << rightdata.results[0].qla_qrb << '\t' << rightdata.results[0].bsa << '\t';
+ out << rightdata.results[0].divr_qlb_qra << '\t' << rightdata.results[0].qlb_qra << '\t' << rightdata.results[0].bsb << '\t';
+
+ out << flag << '\t' << rightdata.results[0].winLStart << "-" << rightdata.results[0].winLEnd << '\t' << rightdata.results[0].winRStart << "-" << rightdata.results[0].winREnd << '\t';
+
+ }else { //print both results
+ if (leftdata.flag == "yes") {
+ out << querySeq.getName() + "_LEFT" << '\t';
+ out << leftdata.results[0].parentA.getName() << "\t" << leftdata.results[0].parentB.getName() << '\t';
+
+ out << leftdata.results[0].divr_qla_qrb << '\t' << leftdata.results[0].qla_qrb << '\t' << leftdata.results[0].bsa << '\t';
+ out << leftdata.results[0].divr_qlb_qra << '\t' << leftdata.results[0].qlb_qra << '\t' << leftdata.results[0].bsb << '\t';
+
+ out << flag << '\t' << leftdata.results[0].winLStart << "-" << leftdata.results[0].winLEnd << '\t' << leftdata.results[0].winRStart << "-" << leftdata.results[0].winREnd << '\t';
+ }
+
+ if (rightdata.flag == "yes") {
+ if (leftdata.flag == "yes") { out << endl; }
+
+ out << querySeq.getName() + "_RIGHT"<< '\t';
+ out << rightdata.results[0].parentA.getName() << "\t" << rightdata.results[0].parentB.getName() << '\t';
+
+ out << rightdata.results[0].divr_qla_qrb << '\t' << rightdata.results[0].qla_qrb << '\t' << rightdata.results[0].bsa << '\t';
+ out << rightdata.results[0].divr_qlb_qra << '\t' << rightdata.results[0].qlb_qra << '\t' << rightdata.results[0].bsb << '\t';
+
+ out << flag << '\t' << rightdata.results[0].winLStart << "-" << rightdata.results[0].winLEnd << '\t' << rightdata.results[0].winRStart << "-" << rightdata.results[0].winREnd << '\t';
+
+ }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "printBlock");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+string ChimeraSlayer::getBlock(data_results leftdata, data_results rightdata, bool leftChimeric, bool rightChimeric, string flag){
+ try {
+
+ string out = "";
+
+ if ((leftChimeric) && (!rightChimeric)) { //get left
+ out += querySeq.getName() + "\t";
+ out += leftdata.results[0].parentA.getName() + "\t" + leftdata.results[0].parentB.getName() + "\t";
+
+ out += toString(leftdata.results[0].divr_qla_qrb) + "\t" + toString(leftdata.results[0].qla_qrb) + "\t" + toString(leftdata.results[0].bsa) + "\t";
+ out += toString(leftdata.results[0].divr_qlb_qra) + "\t" + toString(leftdata.results[0].qlb_qra) + "\t" + toString(leftdata.results[0].bsb) + "\t";
+
+ out += flag + "\t" + toString(leftdata.results[0].winLStart) + "-" + toString(leftdata.results[0].winLEnd) + "\t" + toString(leftdata.results[0].winRStart) + "-" + toString(leftdata.results[0].winREnd) + "\t";
+
+ }else if ((!leftChimeric) && (rightChimeric)) { //print right
+ out += querySeq.getName() + "\t";
+ out += rightdata.results[0].parentA.getName() + "\t" + rightdata.results[0].parentB.getName() + "\t";
+
+ out += toString(rightdata.results[0].divr_qla_qrb) + "\t" + toString(rightdata.results[0].qla_qrb) + "\t" + toString(rightdata.results[0].bsa) + "\t";
+ out += toString(rightdata.results[0].divr_qlb_qra) + "\t" + toString(rightdata.results[0].qlb_qra) + "\t" + toString(rightdata.results[0].bsb) + "\t";
+
+ out += flag + "\t" + toString(rightdata.results[0].winLStart) + "-" + toString(rightdata.results[0].winLEnd) + "\t" + toString(rightdata.results[0].winRStart) + "-" + toString(rightdata.results[0].winREnd) + "\t";
+
+ }else { //print both results
+
+ if (leftdata.flag == "yes") {
+ out += querySeq.getName() + "_LEFT\t";
+ out += leftdata.results[0].parentA.getName() + "\t" + leftdata.results[0].parentB.getName() + "\t";
+
+ out += toString(leftdata.results[0].divr_qla_qrb) + "\t" + toString(leftdata.results[0].qla_qrb) + "\t" + toString(leftdata.results[0].bsa) + "\t";
+ out += toString(leftdata.results[0].divr_qlb_qra) + "\t" + toString(leftdata.results[0].qlb_qra) + "\t" + toString(leftdata.results[0].bsb) + "\t";
+
+ out += flag + "\t" + toString(leftdata.results[0].winLStart) + "-" + toString(leftdata.results[0].winLEnd) + "\t" + toString(leftdata.results[0].winRStart) + "-" + toString(leftdata.results[0].winREnd) + "\t";
+ }
+
+ if (rightdata.flag == "yes") {
+ if (leftdata.flag == "yes") { out += "\n"; }
+ out += querySeq.getName() + "_RIGHT\t";
+ out += rightdata.results[0].parentA.getName() + "\t" + rightdata.results[0].parentB.getName() + "\t";
+
+ out += toString(rightdata.results[0].divr_qla_qrb) + "\t" + toString(rightdata.results[0].qla_qrb) + "\t" + toString(rightdata.results[0].bsa) + "\t";
+ out += toString(rightdata.results[0].divr_qlb_qra) + "\t" + toString(rightdata.results[0].qlb_qra) + "\t" + toString(rightdata.results[0].bsb) + "\t";
+
+ out += flag + "\t" + toString(rightdata.results[0].winLStart) + "-" + toString(rightdata.results[0].winLEnd) + "\t" + toString(rightdata.results[0].winRStart) + "-" + toString(rightdata.results[0].winREnd) + "\t";