exit(1);
}
}
+//***************************************************************************************************************
+Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc, data_results leftPiece, data_results rightPiece) {
+ try {
+ Sequence* trim = NULL;
+
+ if (trimChimera) {
+ string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned();
+ trim = new Sequence(leftPiece.trimQuery.getName(), aligned);
+ }
+
+ if ((leftPiece.flag == "yes") || (rightPiece.flag == "yes")) {
+
+ string chimeraFlag = "no";
+ if (leftPiece.flag == "yes") {
+
+ if( (leftPiece.results[0].bsa >= minBS && leftPiece.results[0].divr_qla_qrb >= divR)
+ ||
+ (leftPiece.results[0].bsb >= minBS && leftPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+ }
+
+ if (rightPiece.flag == "yes") {
+ if ( (rightPiece.results[0].bsa >= minBS && rightPiece.results[0].divr_qla_qrb >= divR)
+ ||
+ (rightPiece.results[0].bsb >= minBS && rightPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+ }
+
+ bool rightChimeric = false;
+ bool leftChimeric = false;
+
+ if (chimeraFlag == "yes") {
+ //which peice is chimeric or are both
+ if (rightPiece.flag == "yes") { if ((rightPiece.results[0].bsa >= minBS) || (rightPiece.results[0].bsb >= minBS)) { rightChimeric = true; } }
+ if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS)) { leftChimeric = true; } }
+
+ if (rightChimeric || leftChimeric) {
+ m->mothurOut(querySeq->getName() + "\tyes"); m->mothurOutEndLine();
+ outAcc << querySeq->getName() << endl;
+
+ if (trimChimera) {
+ string newAligned = trim->getAligned();
+
+ //right side is fine so keep that
+ if ((leftChimeric) && (!rightChimeric)) {
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ }else if ((!leftChimeric) && (rightChimeric)) { //leftside is fine so keep that
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //both sides are chimeric, keep longest piece
+
+ int lengthLeftLeft = leftPiece.spotMap[leftPiece.results[0].winLStart] - leftPiece.spotMap[leftPiece.results[0].winLEnd];
+ int lengthLeftRight = leftPiece.spotMap[leftPiece.results[0].winRStart] - leftPiece.spotMap[leftPiece.results[0].winREnd];
+
+ int longest = 1; // leftleft = 1, leftright = 2, rightleft = 3 rightright = 4
+ int length = lengthLeftLeft;
+ if (lengthLeftLeft < lengthLeftRight) { longest = 2; length = lengthLeftRight; }
+
+ int lengthRightLeft = rightPiece.spotMap[rightPiece.results[0].winLStart] - rightPiece.spotMap[rightPiece.results[0].winLEnd];
+ int lengthRightRight = rightPiece.spotMap[rightPiece.results[0].winRStart] - rightPiece.spotMap[rightPiece.results[0].winREnd];
+
+ if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft; }
+ if (lengthRightRight > length) { longest = 4; }
+
+ if (longest == 1) { //leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else if (longest == 2) { //leftright
+ //get rid of leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winLStart]-1); i < (leftPiece.spotMap[leftPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ //get rid of right
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else if (longest == 3) { //rightleft
+ //get rid of left
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightright
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //rightright
+ //get rid of left
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightleft
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < (rightPiece.spotMap[rightPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ }
+ }
+
+ trim->setAligned(newAligned);
+ }
+
+ }
+ }
+
+ printBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag, out);
+ out << endl;
+ }else { out << querySeq->getName() << "\tno" << endl; }
+
+ return trim;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "print");
+ exit(1);
+ }
+}
+
#ifdef USE_MPI
//***************************************************************************************************************
+Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results leftPiece, data_results rightPiece) {
+ try {
+ MPI_Status status;
+ bool results = false;
+ string outAccString = "";
+ string outputString = "";
+
+ Sequence* trim = NULL;
+
+ if (trimChimera) {
+ string aligned = leftPiece.trimQuery.getAligned() + rightPiece.trimQuery.getAligned();
+ trim = new Sequence(leftPiece.trimQuery.getName(), aligned);
+ }
+
+
+ if ((leftPiece.flag == "yes") || (rightPiece.flag == "yes")) {
+
+ string chimeraFlag = "no";
+ if (leftPiece.flag == "yes") {
+
+ if( (leftPiece.results[0].bsa >= minBS && leftPiece.results[0].divr_qla_qrb >= divR)
+ ||
+ (leftPiece.results[0].bsb >= minBS && leftPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+ }
+
+ if (rightPiece.flag == "yes") {
+ if ( (rightPiece.results[0].bsa >= minBS && rightPiece.results[0].divr_qla_qrb >= divR)
+ ||
+ (rightPiece.results[0].bsb >= minBS && rightPiece.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
+ }
+
+ bool rightChimeric = false;
+ bool leftChimeric = false;
+
+ if (chimeraFlag == "yes") {
+ //which peice is chimeric or are both
+ if (rightPiece.flag == "yes") { if ((rightPiece.results[0].bsa >= minBS) || (rightPiece.results[0].bsb >= minBS)) { rightChimeric = true; } }
+ if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS)) { leftChimeric = true; } }
+
+ if (rightChimeric || leftChimeric) {
+ cout << querySeq->getName() << "\tyes" << endl;
+ outAccString += querySeq->getName() + "\n";
+ results = true;
+
+ //write to accnos file
+ int length = outAccString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outAccString.c_str(), length);
+
+ MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status);
+ delete buf2;
+
+ if (trimChimera) {
+ string newAligned = trim->getAligned();
+
+ //right side is fine so keep that
+ if ((leftChimeric) && (!rightChimeric)) {
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ }else if ((!leftChimeric) && (rightChimeric)) { //leftside is fine so keep that
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //both sides are chimeric, keep longest piece
+
+ int lengthLeftLeft = leftPiece.spotMap[leftPiece.results[0].winLStart] - leftPiece.spotMap[leftPiece.results[0].winLEnd];
+ int lengthLeftRight = leftPiece.spotMap[leftPiece.results[0].winRStart] - leftPiece.spotMap[leftPiece.results[0].winREnd];
+
+ int longest = 1; // leftleft = 1, leftright = 2, rightleft = 3 rightright = 4
+ int length = lengthLeftLeft;
+ if (lengthLeftLeft < lengthLeftRight) { longest = 2; length = lengthLeftRight; }
+
+ int lengthRightLeft = rightPiece.spotMap[rightPiece.results[0].winLStart] - rightPiece.spotMap[rightPiece.results[0].winLEnd];
+ int lengthRightRight = rightPiece.spotMap[rightPiece.results[0].winRStart] - rightPiece.spotMap[rightPiece.results[0].winREnd];
+
+ if (lengthRightLeft > length) { longest = 3; length = lengthRightLeft; }
+ if (lengthRightRight > length) { longest = 4; }
+
+ if (longest == 1) { //leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else if (longest == 2) { //leftright
+ //get rid of leftleft
+ for (int i = (leftPiece.spotMap[leftPiece.results[0].winLStart]-1); i < (leftPiece.spotMap[leftPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ //get rid of right
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else if (longest == 3) { //rightleft
+ //get rid of left
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightright
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winRStart]-1); i < newAligned.length(); i++) { newAligned[i] = '.'; }
+ }else { //rightright
+ //get rid of left
+ for (int i = 0; i < leftPiece.spotMap[leftPiece.results[0].winREnd]; i++) { newAligned[i] = '.'; }
+ //get rid of rightleft
+ for (int i = (rightPiece.spotMap[rightPiece.results[0].winLStart]-1); i < (rightPiece.spotMap[rightPiece.results[0].winLEnd]-1); i++) { newAligned[i] = '.'; }
+ }
+ }
+
+ trim->setAligned(newAligned);
+ }
+
+ }
+ }
+
+ outputString = getBlock(leftPiece, rightPiece, leftChimeric, rightChimeric, chimeraFlag);
+ outputString += "\n";
+
+ //write to output file
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
+ delete buf;
+
+ }else {
+ outputString += querySeq->getName() + "\tno\n";
+
+ //write to output file
+ int length = outputString.length();
+ char* buf = new char[length];
+ memcpy(buf, outputString.c_str(), length);
+
+ MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
+ delete buf;
+ }
+
+
+ return trim;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "print");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
try {
MPI_Status status;
int length = outAccString.length();
char* buf2 = new char[length];
memcpy(buf2, outAccString.c_str(), length);
-
+
MPI_File_write_shared(outAcc, buf2, length, MPI_CHAR, &status);
delete buf2;
outputString = getBlock(chimeraResults[0], chimeraFlag);
outputString += "\n";
- //cout << outputString << endl;
+
//write to output file
int length = outputString.length();
char* buf = new char[length];
memcpy(buf, outputString.c_str(), length);
-
+
MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
delete buf;
-
+
}else {
outputString += querySeq->getName() + "\tno\n";
- //cout << outputString << endl;
+
//write to output file
int length = outputString.length();
char* buf = new char[length];
memcpy(buf, outputString.c_str(), length);
-
+
MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
delete buf;
}
-
return trim;
}
catch(exception& e) {
//***************************************************************************************************************
int ChimeraSlayer::getChimeras(Sequence* query) {
try {
- if (trimChimera) { trimQuery = new Sequence(query->getName(), query->getAligned()); }
+ if (trimChimera) { trimQuery = new Sequence(query->getName(), query->getAligned()); printResults.trimQuery = *trimQuery; }
chimeraFlags = "no";
+ printResults.flag = "no";
//filter query
spotMap = runFilter(query);
+ printResults.spotMap = spotMap;
querySeq = query;
}
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(thisTemplate, match, misMatch);
}
for (itDup = removeDups.begin(); itDup != removeDups.end(); itDup++) {
- //Sequence* seq = getSequence(itDup->first); //makes copy so you can filter and mask and not effect template
itSeq = parentNameSeq.find(itDup->first);
-//cout << itDup->first << itSeq->second << endl;
Sequence* seq = new Sequence(itDup->first, itSeq->second);
SeqDist member;
//put seqs into vector to send to slayer
vector<Sequence*> seqsForSlayer;
+
for (int k = 0; k < seqs.size(); k++) { seqsForSlayer.push_back(seqs[k].seq); }
//mask then send to slayer...
}
if (m->control_pressed) { for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; } return 0; }
-
+
//send to slayer
chimeraFlags = slayer.getResults(query, seqsForSlayer);
if (m->control_pressed) { return 0; }
//free memory
for (int k = 0; k < seqs.size(); k++) { delete seqs[k].seq; }
+
+ printResults.spotMap = spotMap;
+ printResults.flag = chimeraFlags;
+ printResults.results = chimeraResults;
}
- //delete maligner;
- //delete slayer;
-
return 0;
}
catch(exception& e) {
//***************************************************************************************************************
void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
try {
- //out << ":)\n";
-
out << querySeq->getName() << '\t';
out << data.parentA.getName() << "\t" << data.parentB.getName() << '\t';
- //out << "Left Window: " << spotMap[data.winLStart] << " " << spotMap[data.winLEnd] << endl;
- //out << "Right Window: " << spotMap[data.winRStart] << " " << spotMap[data.winREnd] << endl;
-
+
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 << 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;
- //out << "Similarity of query to parentB: " << data.qb << endl;
+ }
+ 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.spotMap[leftdata.results[0].winLStart] << "-" << leftdata.spotMap[leftdata.results[0].winLEnd] << '\t' << leftdata.spotMap[leftdata.results[0].winRStart] << "-" << leftdata.spotMap[leftdata.results[0].winREnd] << '\t';
- //out << "Per_id(QL,A): " << data.qla << endl;
- //out << "Per_id(QL,B): " << data.qlb << endl;
- //out << "Per_id(QR,A): " << data.qra << endl;
- //out << "Per_id(QR,B): " << data.qrb << endl;
-
+ }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.spotMap[rightdata.results[0].winLStart] << "-" << rightdata.spotMap[rightdata.results[0].winLEnd] << '\t' << rightdata.spotMap[rightdata.results[0].winRStart] << "-" << rightdata.spotMap[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.spotMap[leftdata.results[0].winLStart] << "-" << leftdata.spotMap[leftdata.results[0].winLEnd] << '\t' << leftdata.spotMap[leftdata.results[0].winRStart] << "-" << leftdata.spotMap[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.spotMap[rightdata.results[0].winLStart] << "-" << rightdata.spotMap[rightdata.results[0].winLEnd] << '\t' << rightdata.spotMap[rightdata.results[0].winRStart] << "-" << rightdata.spotMap[rightdata.results[0].winREnd] << '\t';
- //out << "DeltaL: " << (data.qla - data.qlb) << endl;
- //out << "DeltaR: " << (data.qra - data.qrb) << endl;
-
+ }
+ }
}
catch(exception& e) {
m->errorOut(e, "ChimeraSlayer", "printBlock");
}
}
//***************************************************************************************************************
+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.spotMap[leftdata.results[0].winLStart]) + "-" + toString(leftdata.spotMap[leftdata.results[0].winLEnd]) + "\t" + toString(leftdata.spotMap[leftdata.results[0].winRStart]) + "-" + toString(leftdata.spotMap[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.spotMap[rightdata.results[0].winLStart]) + "-" + toString(rightdata.spotMap[rightdata.results[0].winLEnd]) + "\t" + toString(rightdata.spotMap[rightdata.results[0].winRStart]) + "-" + toString(rightdata.spotMap[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.spotMap[leftdata.results[0].winLStart]) + "-" + toString(leftdata.spotMap[leftdata.results[0].winLEnd]) + "\t" + toString(leftdata.spotMap[leftdata.results[0].winRStart]) + "-" + toString(leftdata.spotMap[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.spotMap[rightdata.results[0].winLStart]) + "-" + toString(rightdata.spotMap[rightdata.results[0].winLEnd]) + "\t" + toString(rightdata.spotMap[rightdata.results[0].winRStart]) + "-" + toString(rightdata.spotMap[rightdata.results[0].winREnd]) + "\t";
+ }
+ }
+
+ return out;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraSlayer", "getBlock");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
string ChimeraSlayer::getBlock(data_struct data, string flag){
try {
projects / mothur.git / blobdiff