added unix to ifdefs. minor changes while testing 1.24.0.

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 686bdaf4fb43486b87b8f3ad9ba39a874c670ce0..09ff9b5fea6a92ba4a45bb721cb33df9337e7ef6 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -288,7 +288,7 @@ int ScreenSeqsCommand::execute(){
                        getSummary(positions); 
                } 
                else { 
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                 positions = m->divideFile(fastafile, processors);
                 for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
                        #else 
@@ -296,6 +296,7 @@ int ScreenSeqsCommand::execute(){
                 else {
                     int numFastaSeqs = 0;
                     positions = m->setFilePosFasta(fastafile, numFastaSeqs); 
+                    if (positions.size() < processors) { processors = positions.size(); }
                 
                     //figure out how many sequences you have to process
                     int numSeqsPerProcessor = numFastaSeqs / processors;
@@ -611,7 +612,7 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
                vector<int> longHomoPolymer;
                
         vector<unsigned long long> positions;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                positions = m->divideFile(fastafile, processors);
                for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }   
 #else
@@ -619,6 +620,7 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
         else {
             int numFastaSeqs = 0;
             positions = m->setFilePosFasta(fastafile, numFastaSeqs); 
+            if (positions.size() < processors) { processors = positions.size(); }
             
             //figure out how many sequences you have to process
             int numSeqsPerProcessor = numFastaSeqs / processors;
@@ -638,7 +640,7 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
                        driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 #else
                int numSeqs = 0;
-               //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        if(processors == 1){
                                numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
                        }else{
@@ -743,7 +745,7 @@ int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                                count++;
                        }
                        //if((count) % 100 == 0){       m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine();         }
-                       #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
@@ -769,7 +771,7 @@ int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition,
                int num = 0;
                vector<int> processIDS;
 
-#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) {
@@ -1163,7 +1165,7 @@ int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccn
                        count++;
                        }
                        
-                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                                unsigned long long pos = inFASTA.tellg();
                                if ((pos == -1) || (pos >= filePos.end)) { break; }
                        #else
@@ -1275,7 +1277,7 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
         int process = 1;
                int num = 0;
 
-#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) {