added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error...

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index c352feb099a83879bae9e1aca0f35d5bfe56e691..d4e2c752096318748cafa69615a24627f8270aa8 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -531,14 +531,16 @@ int SubSampleCommand::getSubSampleFasta() {
                        string inputString = "fasta=" + outputFileName;
                        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;
+            
                        outputTypes["name"].push_back(filenames["name"][0]);  outputNames.push_back(filenames["name"][0]);
                        m->mothurRemove(outputFileName);
                        outputFileName = filenames["fasta"][0];