fixed indicator grouping problem

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 2dccd498f6dd2e5fdf82a9b12665aaf7a523ad90..abab7a3ddc9dba00b9981cc1df7b464084be902b 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -140,7 +140,9 @@ ChimeraPintailCommand::ChimeraPintailCommand(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;
                                                }
                                        }
@@ -149,7 +151,9 @@ ChimeraPintailCommand::ChimeraPintailCommand(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;
                                                }
                                        }
@@ -196,7 +200,9 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                        if (m->getDefaultPath() != "") { //default path is set
                                                        string tryPath = m->getDefaultPath() + m->getSimpleName(maskfile);
                                                        m->mothurOut("Unable to open " + maskfile + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       ifstream in2;
+                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                       in2.close();
                                                        maskfile = tryPath;
                                        }
                                }
@@ -205,7 +211,9 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                                if (m->getOutputDir() != "") { //default path is set
                                                        string tryPath = m->getOutputDir() + m->getSimpleName(maskfile);
                                                        m->mothurOut("Unable to open " + maskfile + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       ifstream in2;
+                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                       in2.close();
                                                        maskfile = tryPath;
                                                }
                                }
@@ -670,7 +678,11 @@ int ChimeraPintailCommand::createProcesses(string outputFileName, string filenam
                                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