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

[mothur.git] / prcseqscommand.cpp

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index 6a4df6388683b1cda6aa5aa41d1ec3d2d672a15f..c4416b34bf6c8adc444c2292fc03fd140d0b5d0a 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -442,12 +442,12 @@ int PcrSeqsCommand::createProcesses(string filename, string goodFileName, string
                                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){
-                string locationsFile = toString(getpid()) + ".temp";
-                               num = driverPcr(filename, goodFileName + toString(getpid()) + ".temp", badFileName + toString(getpid()) + ".temp", locationsFile, badSeqNames, lines[process], pstart, adjustNeeded);
+                string locationsFile = m->mothurGetpid(process) + ".temp";
+                               num = driverPcr(filename, goodFileName + m->mothurGetpid(process) + ".temp", badFileName + m->mothurGetpid(process) + ".temp", locationsFile, badSeqNames, lines[process], pstart, adjustNeeded);
                                
                                //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 << pstart << '\t' << adjustNeeded << endl;
                                out << num << '\t' << badSeqNames.size() << endl;
@@ -464,7 +464,7 @@ int PcrSeqsCommand::createProcesses(string filename, string goodFileName, string
                        }
                }
                
-        string locationsFile = toString(getpid()) + ".temp";
+        string locationsFile = m->mothurGetpid(process) + ".temp";
         num = driverPcr(filename, goodFileName, badFileName, locationsFile, badSeqNames, lines[0], pstart, adjustNeeded);
         
                //force parent to wait until all the processes are done