working on sra and get.mimarkspackage commands. added file parameter to cluster...

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index bf702e13534f507576bee7c24bcf6462aacb7ca3..ff5f4650c73d3b71c6e76f7398603e711f788859 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -1433,7 +1433,7 @@ int ScreenSeqsCommand::createProcessesContigsSummary(vector<int>& oLength, vecto
         
                //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
@@ -1443,7 +1443,7 @@ int ScreenSeqsCommand::createProcessesContigsSummary(vector<int>& oLength, vecto
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = contigsreport + toString(getpid()) + ".num.temp";
+                               string tempFile = contigsreport + m->mothurGetpid(process) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                
                                out << num << endl;
@@ -1703,7 +1703,7 @@ int ScreenSeqsCommand::createProcessesAlignSummary(vector<float>& sims, vector<f
         
                //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
@@ -1713,7 +1713,7 @@ int ScreenSeqsCommand::createProcessesAlignSummary(vector<float>& sims, vector<f
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = alignreport + toString(getpid()) + ".num.temp";
+                               string tempFile = alignreport + m->mothurGetpid(process) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                
                                out << num << endl;
@@ -1986,7 +1986,7 @@ int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition,
                                
                //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
@@ -1996,7 +1996,7 @@ int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition,
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = fastafile + toString(getpid()) + ".num.temp";
+                               string tempFile = fastafile + m->mothurGetpid(process) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                
                                out << num << endl;
@@ -2526,17 +2526,17 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
                                
                //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(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
+                               num = driver(lines[process], goodFileName + m->mothurGetpid(process) + ".temp", badAccnos + m->mothurGetpid(process) + ".temp", filename, badSeqNames);
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = filename + toString(getpid()) + ".num.temp";
+                               string tempFile = filename + m->mothurGetpid(process) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                out << num << endl;
                                out.close();