*** empty log message ***

diff --git a/bayesian.cpp b/bayesian.cpp
index d62bb23e3e23ae1c98b3757ddd4075b4edf5a806..b1f2c4cf422656bb603f1691b67b79b57305490e 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -111,8 +111,8 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                        //cout << numKmers << '\t' << genusNodes.size() << endl;
                                for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
                        //cout << numKmers << '\t' << genusNodes.size() << endl;        
-                               ofstream out;
-                               ofstream out2;
+                               //ofstream out;
+                               //ofstream out2;
                                
                                #ifdef USE_MPI
                                        int pid;
@@ -122,17 +122,17 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                                #endif
 
                                
-                               m->openOutputFile(probFileName, out);
+                               //m->openOutputFile(probFileName, out);
                                
                                //output mothur version
-                               out << "#" << m->getVersion() << endl;
+                               //out << "#" << m->getVersion() << endl;
                                
-                               out << numKmers << endl;
+                               //out << numKmers << endl;
                                
-                               m->openOutputFile(probFileName2, out2);
+                               //m->openOutputFile(probFileName2, out2);
                                
                                //output mothur version
-                               out2 << "#" << m->getVersion() << endl;
+                               //out2 << "#" << m->getVersion() << endl;
                                
                                #ifdef USE_MPI
                                        }
@@ -149,7 +149,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                                                if (pid == 0) {  
                                        #endif
 
-                                       out << i << '\t';
+                                       //out << i << '\t';
                                        
                                        #ifdef USE_MPI
                                                }
@@ -184,7 +184,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                                                                if (pid == 0) {  
                                                        #endif
 
-                                                       out << k << '\t' << wordGenusProb[i][k] << '\t'; 
+                                                       //out << k << '\t' << wordGenusProb[i][k] << '\t'; 
                                                        
                                                        #ifdef USE_MPI
                                                                }
@@ -200,8 +200,8 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                                                if (pid == 0) {  
                                        #endif
                                        
-                                       out << endl;
-                                       out2 << probabilityInTemplate << '\t' << numNotZero << endl;
+                                       //out << endl;
+                                       //out2 << probabilityInTemplate << '\t' << numNotZero << endl;
                                        
                                        #ifdef USE_MPI
                                                }
@@ -214,8 +214,8 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                                        if (pid == 0) {  
                                #endif
                                
-                               out.close();
-                               out2.close();
+                               //out.close();
+                               //out2.close();
                                
                                #ifdef USE_MPI
                                        }

diff --git a/classify.cpp b/classify.cpp
index 25aa2dd7b9f2f8a4f36030eebf0d3284f7d28b08..c92d9fdc6526788df19d9e6f487ffb641bbaca44 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -61,7 +61,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                        names.push_back(temp.getName());
                                        database->addSequence(temp);    
                                }
-                               database->generateDB();
+//                             database->generateDB();
                        }else if ((method == "kmer") && (!needToGenerate)) {    
                                ifstream kmerFileTest(kmerDBName.c_str());
                                database->readKmerDB(kmerFileTest);     
@@ -150,7 +150,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                        }
                                }
                                
-                               database->generateDB();
+//                             database->generateDB();
                                MPI_File_close(&inMPI);
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                #else
@@ -200,7 +200,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                                }
                                fastaFile.close();
 
-                               database->generateDB();
+//                             database->generateDB();
                                
                        }else if ((method == "kmer") && (!needToGenerate)) {    
                                ifstream kmerFileTest(kmerDBName.c_str());
@@ -223,9 +223,9 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        database->setNumSeqs(names.size());
                        
                        //sanity check
-                       bool okay = phyloTree->ErrorCheck(names);
+                       //bool okay = phyloTree->ErrorCheck(names);
                        
-                       if (!okay) { m->control_pressed = true; }
+                       //if (!okay) { m->control_pressed = true; }
                        
                        m->mothurOut("DONE."); m->mothurOutEndLine();
                        m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();

diff --git a/makefile b/makefile
index 90e495778f99519ceac575c916996f25b2faa3fa..c7dc1fdd1a6aeae18a6db7857a473e2be6fca966 100644 (file)
--- a/makefile
+++ b/makefile
@@ -24,10 +24,10 @@ CXXFLAGS += -O3
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
        #if you are using centos uncomment the following lines
-       #CXX = g++44
+       CXX = g++44
        
        #if you are a mac user use the following line
-       TARGET_ARCH += -arch x86_64
+#      TARGET_ARCH += -arch x86_64
        
        #if you using cygwin to build Windows the following line
        #CXX = x86_64-w64-mingw32-g++
@@ -35,7 +35,7 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
        #TARGET_ARCH += -m64 -static
 
        #if you are a linux user use the following line
-       #CXXFLAGS += -mtune=native -march=native -m64
+       CXXFLAGS += -mtune=native -march=native -m64
        
         CXXFLAGS += -DBIT_VERSION
 endif

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 3c467936a38fbecc55034979a9211ee89c7241b6..13e7ccfd496d035c151eaade308f9832af76b511 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -1501,9 +1501,8 @@ void ShhherCommand::getOTUData(string listFileName){
 
 void ShhherCommand::initPyroCluster(){                          
        try{
-               
                if (numOTUs < processors) { processors = 1; }
-               
+
                dist.assign(numSeqs * numOTUs, 0);
                change.assign(numOTUs, 1);
                centroids.assign(numOTUs, -1);