X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summaryqualcommand.cpp;h=5d7971349656d4400e5d41a24c15e576ccdf57f7;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=0969a1216f3f2152ef21d0e453a6920dff1d663a;hpb=0718c426add1df69adcc24444ef45550fb262ca7;p=mothur.git

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index 0969a12..5d79713 100644
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -45,7 +45,26 @@ string SummaryQualCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string SummaryQualCommand::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 =  "qual.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, "SummaryQualCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 SummaryQualCommand::SummaryQualCommand(){	
 	try {
@@ -111,7 +130,7 @@ 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 +150,12 @@ 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 +181,7 @@ 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 +189,7 @@ 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;
@@ -183,7 +208,7 @@ int SummaryQualCommand::execute(){
 		if (m->control_pressed) {  return 0; }
 		
 		//print summary file
-		string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "qual.summary";
+		string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("summary");
 		printQual(summaryFile, position, averageQ, scores);
 		
 		if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
@@ -262,7 +287,7 @@ 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 +311,7 @@ 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 +393,7 @@ 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 +404,10 @@ 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 +417,18 @@ 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];
 		}