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

[mothur.git] / prcseqscommand.cpp

diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index a1eae4687c4d49b2ce8e0f90895a36a994aec689..ee15bed0a2362a9f9921cd45789ebb83384c0ea5 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -436,18 +436,18 @@ int PcrSeqsCommand::createProcesses(string filename, string goodFileName, string
         
                //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){
-                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;