working on chimera change to add trim feature, fixed bug in print of distance file...

[mothur.git] / chimeraccodecommand.cpp

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 1f6a5a56a8ee7398a8f1b0b454986c28c1483fe7..223ddb23c1bec61748ce62217001dfac04b565ac 100644 (file)
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -125,7 +125,9 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(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;
                                                }
                                        }
@@ -135,7 +137,9 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(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;
                                                }
                                        }
@@ -268,7 +272,7 @@ int ChimeraCcodeCommand::execute(){
                        
                #ifdef USE_MPI
                
-                               int pid, end, numSeqsPerProcessor; 
+                               int pid, numSeqsPerProcessor; 
                                int tag = 2001;
                                vector<unsigned long int> MPIPos;
                                                                
@@ -546,7 +550,7 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
                                        if (m->control_pressed) {       delete candidateSeq; return 1;  }
                
                                        //print results
-                                       bool isChimeric = chimera->print(outMPI, outAccMPI);
+                                       chimera->print(outMPI, outAccMPI);
                                }
                        }
                        delete candidateSeq;
@@ -593,7 +597,11 @@ int ChimeraCcodeCommand::createProcesses(string outputFileName, 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