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

[mothur.git] / makecontigscommand.cpp

diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp
index 8796ab2113f455b12c8eace90df64d4bbe2c318e..72e8ea09aeeac366fc08175dd7019e404020835d 100644 (file)
--- a/makecontigscommand.cpp
+++ b/makecontigscommand.cpp
@@ -704,7 +704,7 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                                        for(int i=0;i<tempFASTAFileNames.size();i++){
                                                for(int j=0;j<tempFASTAFileNames[i].size();j++){
                                                        if (tempFASTAFileNames[i][j] != "") {
-                                                               tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
+                                                               tempFASTAFileNames[i][j] += m->mothurGetpid(process) + ".temp";
                                                                m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
                                                        }
                                                }
@@ -712,14 +712,14 @@ int MakeContigsCommand::createProcesses(vector< vector<string> > files, string o
                                }
                 
                                num = driver(files[process], 
-                             outputFasta + toString(getpid()) + ".temp", 
-                             outputScrapFasta + toString(getpid()) + ".temp", 
-                             outputMisMatches + toString(getpid()) + ".temp",
+                             outputFasta + m->mothurGetpid(process) + ".temp",
+                             outputScrapFasta + m->mothurGetpid(process) + ".temp",
+                             outputMisMatches + m->mothurGetpid(process) + ".temp",
                              tempFASTAFileNames, process, group);
                                
                                //pass groupCounts to parent
                 ofstream out;
-                string tempFile = toString(getpid()) + ".num.temp";
+                string tempFile = m->mothurGetpid(process) + ".num.temp";
                 m->openOutputFile(tempFile, out);
                 out << num << endl;
                                if (createFileGroup || createOligosGroup) {
@@ -1143,7 +1143,7 @@ int MakeContigsCommand::driver(vector<string> files, string outputFasta, string
             num++;
             
                        //report progress
-                       if((num) % 1000 == 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
+                       if((num) % 1000 == 0){  m->mothurOutJustToScreen(toString(num)); m->mothurOutEndLine();         }
                }
         
                //report progress
@@ -1289,7 +1289,7 @@ vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& c
                     count++;
                     
                     //report progress
-                    if((count) % 10000 == 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+                    if((count) % 10000 == 0){  m->mothurOutJustToScreen(toString(count)); m->mothurOutEndLine();               }
                 //}
             }
                }