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 e96b7fd3762fa69c5930066729e867ff69705b3d..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") { 
@@ -420,12 +420,14 @@ int FilterSeqsCommand::filterSequences() {
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                                
 #else
+                       
+               #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;
 
@@ -736,12 +739,14 @@ string FilterSeqsCommand::createFilter() {
                                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
                                
 #else
-               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)
+                               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; }