added unix to ifdefs. minor changes while testing 1.24.0.

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 9913727dcdc8257816e1f83fab2f8a4b903ff1cd..b0fa7a0a2e2f1dbe733207686ec5ed8647ba888e 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -746,7 +746,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                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 >= line.end)) { break; }
                        
@@ -786,7 +786,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                int exitCommand = 1;
                processIDS.clear();
                
-#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) {
                        int pid = fork();
@@ -1027,7 +1027,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                }
                        }
                        
-            #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+            #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                        if(createGroup){
                                ifstream in;
                                string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
@@ -1067,7 +1067,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
         vector<unsigned long long> fastaFilePos;
                vector<unsigned long long> qfileFilePos;
                
-               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                //set file positions for fasta file
                fastaFilePos = m->divideFile(filename, processors);
                
@@ -1157,6 +1157,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
         }else{
             int numFastaSeqs = 0;
             fastaFilePos = m->setFilePosFasta(filename, numFastaSeqs); 
+            if (fastaFilePos.size() < processors) { processors = fastaFilePos.size(); }
         
             if (qfilename != "") { 
                 int numQualSeqs = 0;