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

[mothur.git] / parsimony.cpp

diff --git a/parsimony.cpp b/parsimony.cpp
index 1b08e8a3fe8470e5d34944722e186fdca7e0731b..9ab193fa9bd6ffdbeaa77c71f1c454a0899ba093 100644 (file)
--- a/parsimony.cpp
+++ b/parsimony.cpp
@@ -89,7 +89,7 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
                                
                //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
@@ -102,7 +102,7 @@ EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGr
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = outputDir + toString(getpid()) + ".pars.results.temp";
+                               string tempFile = outputDir + m->mothurGetpid(process) + ".pars.results.temp";
                                m->openOutputFile(tempFile, out);
                                out << myresults.size() << endl;
                                for (int i = 0; i < myresults.size(); i++) {  out << myresults[i] << '\t';  } out << endl;