working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index a12afed8a0d0c0efa8448a55fb3e1d3e0fa450b9..d62bb23e3e23ae1c98b3757ddd4075b4edf5a806 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -19,6 +19,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                
                threadID = tid;
                string baseName = tempFile;
+                       
                if (baseName == "saved") { baseName = rdb->getSavedReference(); }
                
                string baseTName = tfile;
@@ -49,7 +50,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                }
                
                //if you want to save, but you dont need to calculate then just read
-               if (rdb->save && probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood) {  
+               if (rdb->save && probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood && (tempFile != "saved")) {  
                        ifstream saveIn;
                        m->openInputFile(tempFile, saveIn);
                        
@@ -445,8 +446,8 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                #ifdef USE_MPI
                        
                        int pid, num, num2, processors;
-                       vector<unsigned long int> positions;
-                       vector<unsigned long int> positions2;
+                       vector<unsigned long long> positions;
+                       vector<unsigned long long> positions2;
                        
                        MPI_Status status; 
                        MPI_File inMPI;
@@ -575,7 +576,7 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                        string line = m->getline(in); m->gobble(in);
                        
                        in >> numKmers; m->gobble(in);
-                       
+                       //cout << threadID << '\t' << line << '\t' << numKmers << &in << '\t' << &inNum << '\t' << genusNodes.size() << endl;
                        //initialze probabilities
                        wordGenusProb.resize(numKmers);
                        
@@ -588,22 +589,25 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                        
                        //read version
                        string line2 = m->getline(inNum); m->gobble(inNum);
-                       
+               //cout << threadID << '\t' << line2 << '\t' << this << endl;    
                        while (inNum) {
                                inNum >> zeroCountProb[count] >> num[count];  
                                count++;
                                m->gobble(inNum);
+                               //cout << threadID << '\t' << count << endl;
                        }
                        inNum.close();
-               
+               //cout << threadID << '\t' << "here1 " << &wordGenusProb << '\t' << &num << endl; //
+               //cout << threadID << '\t' << &genusTotals << '\t' << endl; 
+               //cout << threadID << '\t' << genusNodes.size() << endl;
                        while(in) {
                                in >> kmer;
-                               
+                       //cout << threadID << '\t' << kmer << endl;
                                //set them all to zero value
                                for (int i = 0; i < genusNodes.size(); i++) {
                                        wordGenusProb[kmer][i] = log(zeroCountProb[kmer] / (float) (genusTotals[i]+1));
                                }
-                               
+                       //cout << threadID << '\t' << num[kmer] << "here" << endl;      
                                //get probs for nonzero values
                                for (int i = 0; i < num[kmer]; i++) {
                                        in >> name >> prob;
@@ -613,7 +617,7 @@ void Bayesian::readProbFile(ifstream& in, ifstream& inNum, string inName, string
                                m->gobble(in);
                        }
                        in.close();
-                       
+               //cout << threadID << '\t' << "here" << endl;   
                #endif
        }
        catch(exception& e) {