fixed clearcut version bug, added group count output to get.groups and remove.groups

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 066a9c51f26b764f14fa3f9490e094748ad3e7b6..024fbab7221c328a02958d34084e4704da55b150 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -32,7 +32,7 @@
 vector<string> ShhherCommand::getValidParameters(){    
        try {
                string Array[] =  {     
-                       "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta"        
+                       "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta", "order"       
                };
                
                vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
@@ -111,7 +111,7 @@ ShhherCommand::ShhherCommand(string option) {
                        
                        //valid paramters for this command
                        string AlignArray[] =  {
-                               "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta"        
+                               "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta", "order"       
                        };
                        
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
@@ -211,6 +211,12 @@ ShhherCommand::ShhherCommand(string option) {
                        temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found")    {       temp = "60";            }
                        convert(temp, sigma); 
                        
+                       flowOrder = validParameter.validFile(parameters, "order", false);
+                       if (flowOrder == "not found"){ flowOrder = "TACG";              }
+                       else if(flowOrder.length() != 4){
+                               m->mothurOut("The value of the order option must be four bases long\n");
+                       }
+                       
                        globaldata = GlobalData::getInstance();
                }
                        
@@ -2010,7 +2016,6 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
 
 void ShhherCommand::writeSequences(vector<int> otuCounts){
        try {
-               string bases = "TACG";
                
                string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.fasta";
                ofstream fastaFile;
@@ -2024,14 +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 = bases[j % 4];
+                                       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();
@@ -2101,7 +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
@@ -2121,15 +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;
                        }