X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=87f51e7c95c136403024c593e681a844ca18d006;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=2b88eb5736bfd37364461facb043b0db76aa3cfc;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 2b88eb5..87f51e7 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -65,6 +65,26 @@ string ChimeraCheckCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ChimeraCheckCommand::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 == "chimera") {  outputFileName =  "chimeracheck.chimeras"; }
+            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, "ChimeraCcodeCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ChimeraCheckCommand::ChimeraCheckCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -281,7 +301,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(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);
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
@@ -306,14 +326,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 			
 			
 			temp = validParameter.validFile(parameters, "ksize", false);			if (temp == "not found") { temp = "7"; }
-			convert(temp, ksize);
+			m->mothurConvert(temp, ksize);
 			
 			temp = validParameter.validFile(parameters, "svg", false);				if (temp == "not found") { temp = "F"; }
 			svg = m->isTrue(temp);
 			if (nameFileNames.size() != 0) { svg = true; }
 			
 			temp = validParameter.validFile(parameters, "increment", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, increment);			
+			m->mothurConvert(temp, increment);			
 		}
 	}
 	catch(exception& e) {
@@ -342,14 +362,14 @@ int ChimeraCheckCommand::execute(){
 			if (m->control_pressed) { delete chimera;	return 0;	}
 			
 			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
-			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
+			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera");
 			outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 			
 		#ifdef USE_MPI
 		
 				int pid, numSeqsPerProcessor; 
 				int tag = 2001;
-				vector<unsigned long int> MPIPos;
+				vector<unsigned long long> MPIPos;
 				
 				MPI_Status status; 
 				MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
@@ -424,14 +444,16 @@ int ChimeraCheckCommand::execute(){
 				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 		#else
 			
-			vector<unsigned long int> positions = m->divideFile(fastaFileNames[i], processors);
-				
-			for (int s = 0; s < (positions.size()-1); s++) {
-				lines.push_back(new linePair(positions[s], positions[(s+1)]));
-			}	
+			
 			
 			//break up file
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+				vector<unsigned long long> positions = m->divideFile(fastaFileNames[i], processors);
+			
+				for (int s = 0; s < (positions.size()-1); s++) {
+					lines.push_back(new linePair(positions[s], positions[(s+1)]));
+				}	
+			
 				if(processors == 1){
 					numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
 					
@@ -459,6 +481,7 @@ int ChimeraCheckCommand::execute(){
 				}
 
 			#else
+				lines.push_back(new linePair(0, 1000));
 				numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
 				
 				if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear(); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} outputTypes.clear(); delete chimera; return 0; }
@@ -519,8 +542,8 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
 			}
 			delete candidateSeq;
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				unsigned long int pos = inFASTA.tellg();
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+				unsigned long long pos = inFASTA.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
 				if (inFASTA.eof()) { break; }
@@ -544,7 +567,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos){
+int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos){
 	try {
 		MPI_File outAccMPI;
 		MPI_Status status; 
@@ -596,7 +619,7 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
 
 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 0;
 		int num = 0;