added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 173227f372f4d4cbf7445e5f3fea440220e70b4a..82c73f3d439c1d3cc154c8dac67398075134a1e8 100644 (file)
--- 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;