corr.axes spearman

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index c463cd294d04dcdc31e1a6891db1659db45dc05e..f5c7bd6876a9d98ed7c9dffa1e4fcd80b76005b2 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -25,6 +25,7 @@ vector<string> FilterSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 FilterSeqsCommand::FilterSeqsCommand(){        
        try {
+               abort = true;
                //initialize outputTypes
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
@@ -132,7 +133,9 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                                                if (m->getDefaultPath() != "") { //default path is set
                                                        string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
                                                        m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       ifstream in2;
+                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                       in2.close();
                                                        fastafileNames[i] = tryPath;
                                                }
                                        }
@@ -142,7 +145,9 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                                                if (m->getOutputDir() != "") { //default path is set
                                                        string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
                                                        m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       ifstream in2;
+                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                       in2.close();
                                                        fastafileNames[i] = tryPath;
                                                }
                                        }
@@ -324,7 +329,7 @@ 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;
                                                
@@ -333,7 +338,6 @@ 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; 
@@ -605,7 +609,11 @@ 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
@@ -969,7 +977,11 @@ 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