X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=filterseqscommand.cpp;h=82c73f3d439c1d3cc154c8dac67398075134a1e8;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=173227f372f4d4cbf7445e5f3fea440220e70b4a;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 173227f..82c73f3 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -222,7 +222,7 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors); 
+			m->mothurConvert(temp, processors); 
 			
 			vertical = validParameter.validFile(parameters, "vertical", false);		
 			if (vertical == "not found") { 
@@ -341,7 +341,7 @@ int FilterSeqsCommand::filterSequences() {
 #ifdef USE_MPI	
 				int pid, numSeqsPerProcessor, num; 
 				int tag = 2001;
-				vector<unsigned long int>MPIPos;
+				vector<unsigned long long>MPIPos;
 						
 				MPI_Status status; 
 				MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
@@ -420,12 +420,14 @@ int FilterSeqsCommand::filterSequences() {
 				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 				
 #else
-			vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
-				
+			
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
+			
 			for (int i = 0; i < (positions.size()-1); i++) {
 				lines.push_back(new linePair(positions[i], positions[(i+1)]));
 			}	
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			
 				if(processors == 1){
 					int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 					numSeqs += numFastaSeqs;
@@ -444,6 +446,7 @@ int FilterSeqsCommand::filterSequences() {
 				
 				if (m->control_pressed) {  return 1; }
 		#else
+				lines.push_back(new linePair(0, 1000));
 				int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 				numSeqs += numFastaSeqs;
 
@@ -462,7 +465,7 @@ int FilterSeqsCommand::filterSequences() {
 }
 #ifdef USE_MPI
 /**************************************************************************************/
-int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {	
+int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {	
 	try {
 		string outputString = "";
 		int count = 0;
@@ -568,7 +571,7 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i
 			}
 			
 			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				unsigned long int pos = in.tellg();
+				unsigned long long pos = in.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
 				if (in.eof()) { break; }
@@ -676,7 +679,7 @@ string FilterSeqsCommand::createFilter() {
 #ifdef USE_MPI	
 				int pid, numSeqsPerProcessor, num; 
 				int tag = 2001;
-				vector<unsigned long int> MPIPos;
+				vector<unsigned long long> MPIPos;
 				
 				MPI_Status status; 
 				MPI_File inMPI; 
@@ -736,12 +739,14 @@ string FilterSeqsCommand::createFilter() {
 				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 				
 #else
-		vector<unsigned long int> positions = m->divideFile(fastafileNames[s], processors);
 				
-		for (int i = 0; i < (positions.size()-1); i++) {
-			lines.push_back(new linePair(positions[i], positions[(i+1)]));
-		}	
+		
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
+				for (int i = 0; i < (positions.size()-1); i++) {
+					lines.push_back(new linePair(positions[i], positions[(i+1)]));
+				}	
+				
 				if(processors == 1){
 					int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 					numSeqs += numFastaSeqs;
@@ -752,6 +757,7 @@ string FilterSeqsCommand::createFilter() {
 				
 				if (m->control_pressed) {  return filterString; }
 		#else
+				lines.push_back(new linePair(0, 1000));
 				int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 				numSeqs += numFastaSeqs;
 				if (m->control_pressed) {  return filterString; }
@@ -877,7 +883,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
 			}
 			
 			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-				unsigned long int pos = in.tellg();
+				unsigned long long pos = in.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
 				if (in.eof()) { break; }
@@ -899,7 +905,7 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
 }
 #ifdef USE_MPI
 /**************************************************************************************/
-int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long int>& MPIPos) {	
+int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long long>& MPIPos) {	
 	try {
 		
 		MPI_Status status;