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

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 31a36f73c6d0339d775dd6a1a4efa8e523c0f14f..988c7112fc1109118f13ed6d45f160930d833dda 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -38,7 +38,7 @@ string ChimeraCheckCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The chimera.check command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
-               helpString += "This command was created using the algorythms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
+               helpString += "This command was created using the algorithms described in CHIMERA_CHECK version 2.7 written by Niels Larsen. \n";
                helpString += "The chimera.check command parameters are fasta, reference, processors, ksize, increment, svg and name.\n";
                helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required unless you have a valid current fasta file. \n";
                helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n";
@@ -628,11 +628,11 @@ int ChimeraCheckCommand::createProcesses(string outputFileName, string filename)
                                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){
-                               num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename);
+                               num = driver(lines[process], outputFileName + toString(m->mothurGetpid(process)) + ".temp", filename);
                                
                                //pass numSeqs to parent
                                ofstream out;
-                               string tempFile = outputFileName + toString(getpid()) + ".num.temp";
+                               string tempFile = outputFileName + toString(m->mothurGetpid(process)) + ".num.temp";
                                m->openOutputFile(tempFile, out);
                                out << num << endl;
                                out.close();