X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerabellerophoncommand.cpp;h=d3c8ea562ea314a6056409671defb41d15f3e834;hp=6d0a116ac4d0d5d1bb2b8cf97f1ea5a1b5126fef;hb=df41d90a9611eab75d0516e2654ed8580f8df24c;hpb=8f909cf6870cc2e4d8ed8cff69a203f6f83a160b

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 6d0a116..d3c8ea5 100644
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -114,7 +114,9 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(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;
 						}
 					}
@@ -124,7 +126,9 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(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;
 						}
 					}