added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / sffmultiplecommand.cpp

diff --git a/sffmultiplecommand.cpp b/sffmultiplecommand.cpp
index f75662b30f258ecf30b3e20e79a76362f633c069..365bb93dc503b65025da52ec2fc11bf21dad5b92 100644 (file)
--- a/sffmultiplecommand.cpp
+++ b/sffmultiplecommand.cpp
@@ -747,17 +747,17 @@ int SffMultipleCommand::createProcesses(vector<string> sffFiles, vector<string>
                
                //loop through and create all the processes you want
                while (process != processors) {
-                       int pid = fork();
+                       pid_t pid = fork();
                        
                        if (pid > 0) {
                                processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
                                process++;
                        }else if (pid == 0){
-                               num = driver(sffFiles, oligosFiles, lines[process].start, lines[process].end, fasta + toString(getpid()) + ".temp", name  + toString(getpid()) + ".temp", group  + toString(getpid()) + ".temp");
+                               num = driver(sffFiles, oligosFiles, lines[process].start, lines[process].end, fasta + m->mothurGetpid(process) + ".temp", name  + m->mothurGetpid(process) + ".temp", group  + m->mothurGetpid(process) + ".temp");
                 
                 //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = toString(getpid()) + ".num.temp";
+                               string tempFile = m->mothurGetpid(process) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                out << num << '\t' << outputNames.size() << endl;
                 for (int i = 0; i < outputNames.size(); i++) {  out << outputNames[i] << endl;  }