fixed classify.seqs output file name - had issue if reference taxonomy file did not...

[mothur.git] / summaryqualcommand.cpp

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index 0969a1216f3f2152ef21d0e453a6920dff1d663a..5c175106ecb2584d07ca15a06c71f27284a3571c 100644 (file)
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -111,7 +111,7 @@ SummaryQualCommand::SummaryQualCommand(string option)  {
                        
                        //check for required parameters
                        qualfile = validParameter.validFile(parameters, "qfile", true);
-                       if (qualfile == "not open") { abort = true; }
+                       if (qualfile == "not open") { qualfile = ""; abort = true; }
                        else if (qualfile == "not found") {                             
                                qualfile = m->getQualFile(); 
                                if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
@@ -131,7 +131,12 @@ SummaryQualCommand::SummaryQualCommand(string option)  {
                        
                        string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);                      
+                       m->mothurConvert(temp, processors);     
+                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(qualfile);
+                               parser.getNameFile(files);
+                       }
                }
        }
        catch(exception& e) {
@@ -157,7 +162,7 @@ int SummaryQualCommand::execute(){
                if (namefile != "") { nameMap = m->readNames(namefile); }
                
                vector<unsigned long long> positions; 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                positions = m->divideFile(qualfile, processors);
                for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(linePair(positions[i], positions[(i+1)]));      }
 #else  
@@ -165,6 +170,7 @@ int SummaryQualCommand::execute(){
                        lines.push_back(linePair(0, 1000)); 
                }else {
                        positions = m->setFilePosFasta(qualfile, numSeqs); 
+            if (positions.size() < processors) { processors = positions.size(); }
                        
                        //figure out how many sequences you have to process
                        int numSeqsPerProcessor = numSeqs / processors;
@@ -262,7 +268,7 @@ int SummaryQualCommand::driverCreateSummary(vector<int>& position, vector<int>&
                                count += num;
                        }
                        
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        unsigned long long pos = in.tellg();
                        if ((pos == -1) || (pos >= filePos.end)) { break; }
 #else
@@ -286,7 +292,7 @@ int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vect
                int numSeqs = 0;
                processIDS.clear();
                
-#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) {
@@ -368,7 +374,7 @@ int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vect
                //////////////////////////////////////////////////////////////////////////////////////////////////////
                //Windows version shared memory, so be careful when passing variables through the seqSumQualData struct. 
                //Above fork() will clone, so memory is separate, but that's not the case with windows, 
-               //Taking advantage of shared memory to allow both threads to add info to vectors.
+               //Taking advantage of shared memory to pass results vectors.
                //////////////////////////////////////////////////////////////////////////////////////////////////////
                
                vector<seqSumQualData*> pDataArray; 
@@ -379,12 +385,10 @@ int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vect
                for( int i=0; i<processors; i++ ){
                        
                        // Allocate memory for thread data.
-                       seqSumQualData* tempSum = new seqSumQualData(&position, &averageQ, &scores, filename, m, lines[i].start, lines[i].end, namefile, nameMap);
+                       seqSumQualData* tempSum = new seqSumQualData(filename, m, lines[i].start, lines[i].end, namefile, nameMap);
                        pDataArray.push_back(tempSum);
                        processIDS.push_back(i);
-                       
-                       //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
-                       //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+        
                        hThreadArray[i] = CreateThread(NULL, 0, MySeqSumQualThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);   
                }
                
@@ -394,6 +398,18 @@ int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vect
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        numSeqs += pDataArray[i]->count;
+            int tempNum = pDataArray[i]->position.size();
+            if (position.size() < tempNum) { position.resize(tempNum, 0); }
+                       if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }
+                       if (scores.size() < tempNum) { 
+                               scores.resize(tempNum); 
+                               for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
+                       }
+            
+            for (int k = 0; k < tempNum; k++)                  {                position[k]    +=  pDataArray[i]->position[k];         }               
+                       for (int k = 0; k < tempNum; k++)                       {                averageQ[k]    +=  pDataArray[i]->averageQ[k];         }               
+                       for (int k = 0; k < tempNum; k++)                       {       for (int j = 0; j < 41; j++) {  scores[k][j] += pDataArray[i]->scores[k][j];   }        }
+
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }