random chagnes from pat

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index b21d4140b84280251cb208705bf0fca70919d0e0..024fbab7221c328a02958d34084e4704da55b150 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -2016,7 +2016,6 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
 
 void ShhherCommand::writeSequences(vector<int> otuCounts){
        try {
-               flowOrder = "TACG";
                
                string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.fasta";
                ofstream fastaFile;
@@ -2030,14 +2029,17 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
                        if(otuCounts[i] > 0){
                                fastaFile << '>' << seqNameVector[aaI[i][0]] << endl;
                                
-                               for(int j=8;j<numFlowCells;j++){
+                               string newSeq = "";
+                               
+                               for(int j=0;j<numFlowCells;j++){
                                        
                                        char base = flowOrder[j % 4];
                                        for(int k=0;k<uniqueFlowgrams[index * numFlowCells + j];k++){
-                                               fastaFile << base;
+                                               newSeq += base;
                                        }
                                }
-                               fastaFile << endl;
+                               
+                               fastaFile << newSeq.substr(4) << endl;
                        }
                }
                fastaFile.close();
@@ -2107,7 +2109,7 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
                ofstream otuCountsFile;
                m->openOutputFile(otuCountsFileName, otuCountsFile);
                
-               string bases = "TACG";
+               string bases = flowOrder;
                
                for(int i=0;i<numOTUs;i++){
                        //output the translated version of the centroid sequence for the otu
@@ -2127,15 +2129,18 @@ void ShhherCommand::writeClusters(vector<int> otuCounts){
                                        int sequence = aaI[i][j];
                                        otuCountsFile << seqNameVector[sequence] << '\t';
                                        
-                                       for(int k=8;k<lengths[sequence];k++){
+                                       string newSeq = "";
+                                       
+                                       for(int k=0;k<lengths[sequence];k++){
                                                char base = bases[k % 4];
                                                int freq = int(0.01 * (double)flowDataIntI[sequence * numFlowCells + k] + 0.5);
-                                               
+                                                       
                                                for(int s=0;s<freq;s++){
-                                                       otuCountsFile << base;
+                                                       newSeq += base;
+                                                       //otuCountsFile << base;
                                                }
                                        }
-                                       otuCountsFile << endl;
+                                       otuCountsFile << newSeq.substr(4) << endl;
                                }
                                otuCountsFile << endl;
                        }