changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / shhhseqscommand.cpp

diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 72504196039c9f337f8051ecdf54a4af1eed5c90..5c6359ec58bb776ce9a050a132e8409e60cf197b 100644 (file)
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -364,7 +364,7 @@ vector<string> ShhhSeqsCommand::createProcessesGroups(SequenceParser& parser, st
                        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) {
@@ -695,14 +695,15 @@ int ShhhSeqsCommand::deconvoluteResults(string fastaFile, string nameFile){
                string inputString = "fasta=" + fastaFile + ", name=" + nameFile;
                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(); 
                
                string newnameFile = filenames["name"][0];