X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=b9436f8078df0da22408dafc889d16e62d8a7d6c;hb=bdb5d82e2a73829b4e1fa42656ad9bcb57e3e948;hp=c463cd294d04dcdc31e1a6891db1659db45dc05e;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index c463cd2..b9436f8 100644
--- 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;
 						}
 					}
@@ -605,7 +610,11 @@ 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 +978,11 @@ 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