chimera->getChimeras(candidateSeq);
if (m->control_pressed) { delete candidateSeq; return 1; }
-
- //do you want to check both pieces for chimeras
- if (trimera) {
- //if you are not chimeric, then check each half
- data_results wholeResults = chimera->getResults();
+ //if you are not chimeric, then check each half
+ data_results wholeResults = chimera->getResults();
+
+ //determine if we need to split
+ bool isChimeric = false;
+
+ if (wholeResults.flag == "yes") {
+ string chimeraFlag = "no";
+ if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
+ ||
+ (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
- //determine if we need to split
- bool isChimeric = false;
- if (wholeResults.flag == "yes") {
- string chimeraFlag = "no";
- if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
- ||
- (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
-
-
- if (chimeraFlag == "yes") {
- if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
- }
+ if (chimeraFlag == "yes") {
+ if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
}
+ }
+
+ if ((!isChimeric) && trimera) {
- if (!isChimeric) {
-
- //split sequence in half by bases
- string leftQuery, rightQuery;
- Sequence tempSeq(candidateSeq->getName(), candidateAligned);
- divideInHalf(tempSeq, leftQuery, rightQuery);
-
- //run chimeraSlayer on each piece
- Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
- Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
-
- //find chimeras
- chimera->getChimeras(left);
- data_results leftResults = chimera->getResults();
-
- chimera->getChimeras(right);
- data_results rightResults = chimera->getResults();
-
- //if either piece is chimeric then report
- Sequence* trimmed = chimera->print(out, out2, leftResults, rightResults);
- if (trim) { trimmed->printSequence(out3); delete trimmed; }
-
- delete left; delete right;
-
- }else { //already chimeric
- //print results
- Sequence* trimmed = chimera->print(out, out2);
- if (trim) { trimmed->printSequence(out3); delete trimmed; }
- }
- }else {
+ //split sequence in half by bases
+ string leftQuery, rightQuery;
+ Sequence tempSeq(candidateSeq->getName(), candidateAligned);
+ divideInHalf(tempSeq, leftQuery, rightQuery);
+
+ //run chimeraSlayer on each piece
+ Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
+ Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
+
+ //find chimeras
+ chimera->getChimeras(left);
+ data_results leftResults = chimera->getResults();
+
+ chimera->getChimeras(right);
+ data_results rightResults = chimera->getResults();
+
+ //if either piece is chimeric then report
+ Sequence* trimmed = chimera->print(out, out2, leftResults, rightResults);
+ if (trim) { trimmed->printSequence(out3); delete trimmed; }
+
+ delete left; delete right;
+
+ }else { //already chimeric
//print results
Sequence* trimmed = chimera->print(out, out2);
if (trim) { trimmed->printSequence(out3); delete trimmed; }
}
+
}
count++;
}
if (m->control_pressed) { delete candidateSeq; return 1; }
- //do you want to check both pieces for chimeras
- if (trimera) {
-
- //if you are not chimeric, then check each half
- data_results wholeResults = chimera->getResults();
+ //if you are not chimeric, then check each half
+ data_results wholeResults = chimera->getResults();
+
+ //determine if we need to split
+ bool isChimeric = false;
+
+ if (wholeResults.flag == "yes") {
+ string chimeraFlag = "no";
+ if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
+ ||
+ (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
- //determine if we need to split
- bool isChimeric = false;
- if (wholeResults.flag == "yes") {
- string chimeraFlag = "no";
- if( (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
- ||
- (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
-
-
- if (chimeraFlag == "yes") {
- if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
- }
+ if (chimeraFlag == "yes") {
+ if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
}
+ }
+
+ if ((!isChimeric) && trimera) {
+ //split sequence in half by bases
+ string leftQuery, rightQuery;
+ Sequence tempSeq(candidateSeq->getName(), candidateAligned);
+ divideInHalf(tempSeq, leftQuery, rightQuery);
- if (!isChimeric) {
- //split sequence in half by bases
- string leftQuery, rightQuery;
- Sequence tempSeq(candidateSeq->getName(), candidateAligned);
- divideInHalf(tempSeq, leftQuery, rightQuery);
-
- //run chimeraSlayer on each piece
- Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
- Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
-
- //find chimeras
- chimera->getChimeras(left);
- data_results leftResults = chimera->getResults();
-
- chimera->getChimeras(right);
- data_results rightResults = chimera->getResults();
-
- //if either piece is chimeric then report
- Sequence* trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
- if (trim) {
- string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
- delete trimmed;
-
- //write to accnos file
- int length = outputString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outputString.c_str(), length);
-
- MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
- }
-
- delete left; delete right;
+ //run chimeraSlayer on each piece
+ Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
+ Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
+
+ //find chimeras
+ chimera->getChimeras(left);
+ data_results leftResults = chimera->getResults();
+
+ chimera->getChimeras(right);
+ data_results rightResults = chimera->getResults();
+
+ //if either piece is chimeric then report
+ Sequence* trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
+ if (trim) {
+ string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
+ delete trimmed;
- }else { //already chimeric
- //print results
- Sequence* trimmed = chimera->print(outMPI, outAccMPI);
+ //write to accnos file
+ int length = outputString.length();
+ char* buf2 = new char[length];
+ memcpy(buf2, outputString.c_str(), length);
- if (trim) {
- string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
- delete trimmed;
-
- //write to accnos file
- int length = outputString.length();
- char* buf2 = new char[length];
- memcpy(buf2, outputString.c_str(), length);
-
- MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
- delete buf2;
- }
+ MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
+ delete buf2;
}
- }else {
+
+ delete left; delete right;
+
+ }else {
//print results
Sequence* trimmed = chimera->print(outMPI, outAccMPI);
projects / mothur.git / blobdiff