added namefile to summary.seqs

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index c4a3a95fe7d2cff8948650ebabea4290fbaa742a..6fd4e04a0e562e5ee44fd0a05fc7df9b1bfae3d4 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -25,8 +25,7 @@ vector<string> FilterSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 FilterSeqsCommand::FilterSeqsCommand(){        
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["filter"] = tempOutNames;
@@ -62,11 +61,11 @@ vector<string> FilterSeqsCommand::getRequiredFiles(){
 /**************************************************************************************/
 FilterSeqsCommand::FilterSeqsCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                filterFileName = "";
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -240,7 +239,7 @@ void FilterSeqsCommand::help(){
 int FilterSeqsCommand::execute() {     
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                ifstream inFASTA;
                m->openInputFile(fastafileNames[0], inFASTA);
@@ -329,7 +328,7 @@ int FilterSeqsCommand::filterSequences() {
                                
                                string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 #ifdef USE_MPI 
-                               int pid, start, end, numSeqsPerProcessor, num; 
+                               int pid, numSeqsPerProcessor, num; 
                                int tag = 2001;
                                vector<unsigned long int>MPIPos;
                                                
@@ -338,7 +337,6 @@ int FilterSeqsCommand::filterSequences() {
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
                                
                                MPI_File outMPI;
-                               MPI_File tempMPI;
                                MPI_File inMPI;
                                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                                int inMode=MPI_MODE_RDONLY; 
@@ -610,7 +608,11 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
                                out.close();
                                
                                exit(0);
-                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                       }else { 
+                               m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+                               for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                               exit(0);
+                       }
                }
                
                //force parent to wait until all the processes are done
@@ -974,7 +976,11 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
                                out.close();
                                
                                exit(0);
-                       }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+                       }else { 
+                               m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+                               for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+                               exit(0);
+                       }
                }
                
                //parent do your part