added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / chimeraperseuscommand.cpp

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index 76f0103c38ec64a5ebc21f3175df441a15ccae0e..e7294a854ec4134ccad5e17aa0ed8abb51876d09 100644 (file)
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -466,14 +466,15 @@ string ChimeraPerseusCommand::getNamesFile(string& inputFile){
                string inputString = "fasta=" + inputFile;
                m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-               
+               m->mothurCalling = true;
+        
                Command* uniqueCommand = new DeconvoluteCommand(inputString);
                uniqueCommand->execute();
                
                map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
                
                delete uniqueCommand;
-               
+               m->mothurCalling = false;
                m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
                
                nameFile = filenames["name"][0];
@@ -768,7 +769,7 @@ int ChimeraPerseusCommand::createProcessesGroups(SequenceParser& parser, string
                        lines.push_back(linePair(startIndex, endIndex));
                }
                
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)          
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)         
                
                //loop through and create all the processes you want
                while (process != processors) {