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

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 951ce65d400bb36afc60df92e56e148c14ee271c..7f2a85287099cfafd8731b3055b232dfbad4a00f 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -1047,15 +1047,15 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                        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();
 
                                                                if(qFileName != ""){
-                                                                       tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
+                                                                       tempPrimerQualFileNames[i][j] += m->mothurGetpid(process) + ".temp";
                                                                        m->openOutputFile(tempPrimerQualFileNames[i][j], temp);         temp.close();
                                                                }
                                                                if(nameFile != ""){
-                                                                       tempNameFileNames[i][j] += toString(getpid()) + ".temp";
+                                                                       tempNameFileNames[i][j] += m->mothurGetpid(process) + ".temp";
                                                                        m->openOutputFile(tempNameFileNames[i][j], temp);               temp.close();
                                                                }
                                                        }
@@ -1065,27 +1065,27 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                                        
                                driverCreateTrim(filename,
                                                                 qFileName,
-                                                                (trimFASTAFileName + toString(getpid()) + ".temp"),
-                                                                (scrapFASTAFileName + toString(getpid()) + ".temp"),
-                                                                (trimQualFileName + toString(getpid()) + ".temp"),
-                                                                (scrapQualFileName + toString(getpid()) + ".temp"),
-                                                                (trimNameFileName + toString(getpid()) + ".temp"),
-                                                                (scrapNameFileName + toString(getpid()) + ".temp"),
-                                 (trimCountFileName + toString(getpid()) + ".temp"),
-                                                                (scrapCountFileName + toString(getpid()) + ".temp"),
-                                                                (groupFile + toString(getpid()) + ".temp"),
+                                                                (trimFASTAFileName + m->mothurGetpid(process) + ".temp"),
+                                                                (scrapFASTAFileName + m->mothurGetpid(process) + ".temp"),
+                                                                (trimQualFileName + m->mothurGetpid(process) + ".temp"),
+                                                                (scrapQualFileName + m->mothurGetpid(process) + ".temp"),
+                                                                (trimNameFileName + m->mothurGetpid(process) + ".temp"),
+                                                                (scrapNameFileName + m->mothurGetpid(process) + ".temp"),
+                                 (trimCountFileName + m->mothurGetpid(process) + ".temp"),
+                                                                (scrapCountFileName + m->mothurGetpid(process) + ".temp"),
+                                                                (groupFile + m->mothurGetpid(process) + ".temp"),
                                                                 tempFASTAFileNames,
                                                                 tempPrimerQualFileNames,
                                                                 tempNameFileNames,
                                                                 lines[process],
                                                                 qLines[process]);
                 
-                if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + toString(getpid()) + '\n'); }
+                if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + m->mothurGetpid(process) + '\n'); }
                                
                                //pass groupCounts to parent
                                if(createGroup){
                                        ofstream out;
-                                       string tempFile = filename + toString(getpid()) + ".num.temp";
+                                       string tempFile = filename + m->mothurGetpid(process) + ".num.temp";
                                        m->openOutputFile(tempFile, out);
                                        
                                        out << groupCounts.size() << endl;