trim.seqs linker and spacer mods

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index c2ea5346125d31ed6779b1b7f20c9280a79678c1..f5ef635f6eb6e223e72e8f2e50f23eb041f447a5 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -149,10 +149,10 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
-                       convert(temp, minFlows);  
+                       m->mothurConvert(temp, minFlows);  
 
                        temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
-                       convert(temp, maxFlows);  
+                       m->mothurConvert(temp, maxFlows);  
                        
                        
                        temp = validParameter.validFile(parameters, "oligos", true);
@@ -164,28 +164,28 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        else if(m->isTrue(temp))        {       fasta = 1;      }
                        
                        temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found"){       temp = "9";             }
-                       convert(temp, maxHomoP);  
+                       m->mothurConvert(temp, maxHomoP);  
 
                        temp = validParameter.validFile(parameters, "signal", false);           if (temp == "not found"){       temp = "0.50";  }
-                       convert(temp, signal);  
+                       m->mothurConvert(temp, signal);  
 
                        temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
-                       convert(temp, noise);  
+                       m->mothurConvert(temp, noise);  
        
                        temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
-                       convert(temp, bdiffs);
+                       m->mothurConvert(temp, bdiffs);
                        
                        temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
-                       convert(temp, pdiffs);
+                       m->mothurConvert(temp, pdiffs);
                        
                        temp = validParameter.validFile(parameters, "tdiffs", false);
                        if (temp == "not found"){ int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
-                       convert(temp, tdiffs);
+                       m->mothurConvert(temp, tdiffs);
                        if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
        
                        flowOrder = validParameter.validFile(parameters, "order", false);
                        if (flowOrder == "not found"){ flowOrder = "TACG";              }
@@ -295,7 +295,7 @@ int TrimFlowsCommand::execute(){
                                                        m->mothurRemove(barcodePrimerComboFileNames[i][j]);
                                                }
                                                else{
-                                                       output << barcodePrimerComboFileNames[i][j] << endl;
+                                                       output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
                                                        outputNames.push_back(barcodePrimerComboFileNames[i][j]);
                                                        outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
                                                }
@@ -309,7 +309,7 @@ int TrimFlowsCommand::execute(){
                        flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
                        m->openOutputFile(flowFilesFileName, output);
                        
-                       output << trimFlowFileName << endl;
+                       output << m->getFullPathName(trimFlowFileName) << endl;
                        
                        output.close();
                }