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 a1eae4687c4d49b2ce8e0f90895a36a994aec689..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
@@ -575,7 +575,7 @@ int PcrSeqsCommand::createProcesses(string filename, string goodFileName, string
         
         
 
-        if (fileAligned) {
+        if (fileAligned && adjustNeeded) {
             //find pend - pend is the biggest ending value, but we must account for when we adjust the start.  That adjustment may make the "new" end larger then the largest end. So lets find out what that "new" end will be.
             ifstream inLocations;
             m->openInputFile(locationsFile, inLocations);
@@ -608,7 +608,7 @@ int PcrSeqsCommand::createProcesses(string filename, string goodFileName, string
             inLocations.close();
             
             adjustDots(goodFileName, locationsFile, pstart, pend);
-        }
+        }else { m->mothurRemove(locationsFile); }
         
         return num;