changed int to pid_t type in fork(). roughed in get.mimarkscommand.

[mothur.git] / chimerauchimecommand.cpp

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 7a48cf70d092f7d05c8b3bc3656bd66bf17c02d8..d7df400d1c70cd8842dd48120f5d9974311ad87d 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -1633,17 +1633,17 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
                                
                //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(outputFileName + toString(getpid()) + ".temp", files[process], accnos + toString(getpid()) + ".temp", alns + toString(getpid()) + ".temp", numChimeras);
+                               num = driver(outputFileName + toString(m->mothurGetpid(process)) + ".temp", files[process], accnos + toString(m->mothurGetpid(process)) + ".temp", alns + toString(m->mothurGetpid(process)) + ".temp", numChimeras);
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = outputFileName + toString(getpid()) + ".num.temp";
+                               string tempFile = outputFileName + toString(m->mothurGetpid(process)) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                out << num << endl;
                                out << numChimeras << endl;
@@ -1817,17 +1817,17 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
                                
                //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 = driverGroups(outputFName + toString(getpid()) + ".temp", filename + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", alns + toString(getpid()) + ".temp", accnos + ".byCount." + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
+                               num = driverGroups(outputFName + toString(m->mothurGetpid(process)) + ".temp", filename + toString(m->mothurGetpid(process)) + ".temp", accnos + toString(m->mothurGetpid(process)) + ".temp", alns + toString(m->mothurGetpid(process)) + ".temp", accnos + ".byCount." + toString(m->mothurGetpid(process)) + ".temp", lines[process].start, lines[process].end, groups);
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = outputFName + toString(getpid()) + ".num.temp";
+                               string tempFile = outputFName + toString(m->mothurGetpid(process)) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                out << num << endl;
                                out.close();