pds' small change to sffinfo

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 2c4f7fba4253c2cb4c2693bb3cb18e676c5d938b..b92e8c8d355f6d105c141857bd96c19538ba194b 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -196,7 +196,7 @@ int ChimeraSlayer::print(ostream& out, ostream& outAcc) {
                                }
                        }
                        
-                       printBlock(chimeraResults[0], out);
+                       printBlock(chimeraResults[0], chimeraFlag, out);
                        out << endl;
                }else {  out << querySeq->getName() << "\tno" << endl;  }
                
@@ -240,7 +240,7 @@ int ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
                                }
                        }
                        
-                       outputString = getBlock(chimeraResults[0]);
+                       outputString = getBlock(chimeraResults[0], chimeraFlag);
                        outputString += "\n";
        //cout << outputString << endl;         
                        //write to output file
@@ -286,13 +286,13 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                //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);
@@ -387,7 +387,7 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
        }
 }
 //***************************************************************************************************************
-void ChimeraSlayer::printBlock(data_struct data, ostream& out){
+void ChimeraSlayer::printBlock(data_struct data, string flag, ostream& out){
        try {
        //out << ":)\n";
                
@@ -399,7 +399,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
                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;
@@ -422,7 +422,7 @@ void ChimeraSlayer::printBlock(data_struct data, ostream& out){
        }
 }
 //***************************************************************************************************************
-string ChimeraSlayer::getBlock(data_struct data){
+string ChimeraSlayer::getBlock(data_struct data, string flag){
        try {
                
                string outputString = "";
@@ -433,7 +433,7 @@ string ChimeraSlayer::getBlock(data_struct data){
                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;
        }