added debug statements to trim.seqs

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 37d0fdfe10fdbe3eb11d3c7f74cbc84389acead9..c328a041267d01e21ed2e99780f18de486571685 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -45,6 +45,26 @@ string SeqSummaryCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string SeqSummaryCommand::getOutputFileNameTag(string type, string inputName=""){      
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "summary")            {   outputFileName =  "summary";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SeqSummaryCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************
 SeqSummaryCommand::SeqSummaryCommand(){        
@@ -155,7 +175,7 @@ int SeqSummaryCommand::execute(){
                //set current fasta to fastafile
                m->setFastaFile(fastafile);
                
-               string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
+               string summaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
                                
                int numSeqs = 0;
                
@@ -286,11 +306,12 @@ int SeqSummaryCommand::execute(){
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else
                        vector<unsigned long long> positions; 
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                positions = m->divideFile(fastafile, processors);
                                for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
                        #else
                                positions = m->setFilePosFasta(fastafile, numSeqs); 
+                if (positions.size() < processors) { processors = positions.size(); }
                
                                //figure out how many sequences you have to process
                                int numSeqsPerProcessor = numSeqs / processors;
@@ -413,7 +434,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                                        //make sure this sequence is in the namefile, else error 
                                        map<string, int>::iterator it = nameMap.find(current.getName());
                                        
-                                       if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+                                       if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
                                        else { num = it->second; }
                                }
                                
@@ -433,7 +454,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                                outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
                        }
                        
-                       #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
@@ -529,7 +550,7 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
                int num = 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) {
@@ -612,7 +633,7 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
             string extension = "";
             if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
                        // Allocate memory for thread data.
-                       seqSumData* tempSum = new seqSumData(&startPosition, &endPosition, &seqLength, &ambigBases, &longHomoPolymer, filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, namefile, nameMap);
+                       seqSumData* tempSum = new seqSumData(filename, (sumFile+extension), m, lines[i]->start, lines[i]->end, namefile, nameMap);
                        pDataArray.push_back(tempSum);
                        
                        //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
@@ -630,6 +651,11 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
                        num += pDataArray[i]->count;
+            for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {    startPosition.push_back(pDataArray[i]->startPosition[k]);       }
+                       for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {   endPosition.push_back(pDataArray[i]->endPosition[k]);       }
+            for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) {        seqLength.push_back(pDataArray[i]->seqLength[k]);       }
+            for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) {       ambigBases.push_back(pDataArray[i]->ambigBases[k]);       }
+            for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) {  longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]);       }
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }