update .gitignore

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 7adf82814ee5447edef7e203bbb046ad61c51b07..b266025f1720d5c0ef7366d1ee7d155182f3fa21 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -38,7 +38,7 @@ string ChimeraCcodeCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The chimera.ccode command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
-               helpString += "This command was created using the algorythms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n";
+               helpString += "This command was created using the algorithms described in the 'Evaluating putative chimeric sequences from PCR-amplified products' paper by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez.\n";
                helpString += "The chimera.ccode command parameters are fasta, reference, filter, mask, processors, window and numwanted.\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";
@@ -548,10 +548,10 @@ int ChimeraCcodeCommand::driver(linePair* filePos, string outputFName, string fi
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");             }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen("Processing sequence: " + toString(count) + "\n");     }
                
                out.close();
                out2.close();
@@ -633,17 +633,17 @@ int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename,
                
                //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){
-                               num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp");
+                               num = driver(lines[process], outputFileName + toString(m->mothurGetpid(process)) + ".temp", filename, accnos + toString(m->mothurGetpid(process)) + ".temp");
                                
                                //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();