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

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 6caa606dc10ee387cd2eb829d264a7d17f0ee670..ab079fd073ccd0463b55e909cab4d4d46e7f1bc3 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";
@@ -547,11 +547,10 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
-            count++;
+                       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();
                inFASTA.close();
@@ -599,10 +598,10 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
                        delete candidateSeq;
                        
                        //report progress
-                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
+                       if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;                }
                }
                //report progress
-               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
+               if(num % 100 != 0){             cout << "Processing sequence: " << num << endl;         }
                
                return 0;
        }
@@ -623,17 +622,17 @@ int ChimeraCheckCommand::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);
+                               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();