testing 1.14.0

[mothur.git] / degapseqscommand.cpp

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 290d5dc0996a62783ab3365513f7441b1aafd717..f1190c84ad58a73b66b3423cbf2d10cee907bb93 100644 (file)
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -112,7 +112,9 @@ DegapSeqsCommand::DegapSeqsCommand(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;
                                                }
                                        }
@@ -122,7 +124,9 @@ DegapSeqsCommand::DegapSeqsCommand(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;
                                                }
                                        }