added mothurgetpid function. fixed bug with align.seqs related to g++ 4.8 change...

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index e7dc92e5919d1f5f7078fd5a11171cbb39030861..9a2b249ce213bb97096b94a41bc36d54f9919d30 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -1583,11 +1583,11 @@ int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accno
                                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", accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", breakUp[process], fileGroup, accnos + toString(getpid()) + ".byCount");
+                               num = driverGroups(outputFName + toString(m->mothurGetpid(process)) + ".temp", accnos + m->mothurGetpid(process) + ".temp", fasta + toString(m->mothurGetpid(process)) + ".temp", breakUp[process], fileGroup, accnos + toString(m->mothurGetpid(process)) + ".byCount");
                                
                                //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();
@@ -1714,6 +1714,8 @@ int ChimeraSlayerCommand::createProcessesGroups(string outputFName, string accno
 int ChimeraSlayerCommand::driver(linePair filePos, string outputFName, string filename, string accnos, string fasta, map<string, int>& priority){
        try {
                
+        if (m->debug) { m->mothurOut("[DEBUG]: filename = " + filename + "\n"); }
+        
                Chimera* chimera;
                if (templatefile != "self") { //you want to run slayer with a reference template
                        chimera = new ChimeraSlayer(filename, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, rand());       
@@ -1998,6 +2000,8 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
                int process = 0;
                int num = 0;
                processIDS.clear();
+        
+        if (m->debug) { m->mothurOut("[DEBUG]: filename = " + filename + "\n"); }
                
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
                //loop through and create all the processes you want
@@ -2008,11 +2012,11 @@ int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename
                                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], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp", thisPriority);
+                               num = driver(lines[process], outputFileName + toString(m->mothurGetpid(process)) + ".temp", filename, accnos + toString(m->mothurGetpid(process)) + ".temp", fasta + toString(m->mothurGetpid(process)) + ".temp", thisPriority);
                                
                                //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.close();