testing 1.14.0

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index cfe9d509112e921aef92c0cf914e10f6ca885079..4b263b491c59c0cd14abaf0d4553ffa20fdd26f6 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -214,7 +214,7 @@ bool ValidParameters::isValidParameter(string parameter, vector<string> cParams,
 string ValidParameters::validFile(map<string, string>& container, string parameter, bool isFile) {
        try {
                int ableToOpen;
-               ifstream in;
+               
                map<string, string>::iterator it;
                
                it = container.find(parameter);
@@ -232,15 +232,18 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
                                
                                if (pid == 0) {
                        #endif
-
+                               ifstream in;
                                ableToOpen = m->openInputFile(it->second, in, "noerror");
+                               in.close();
                                
                                //if you can't open it, try default location
                                if (ableToOpen == 1) {
                                        if (m->getDefaultPath() != "") { //default path is set
                                                string tryPath = m->getDefaultPath() + m->getSimpleName(it->second);
                                                m->mothurOut("Unable to open " + it->second + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                               ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                               ifstream in2;
+                                               ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                               in2.close();
                                                container[parameter] = tryPath;
                                        }
                                }
@@ -250,12 +253,14 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
                                        if (m->getOutputDir() != "") { //default path is set
                                                string tryPath = m->getOutputDir() + m->getSimpleName(it->second);
                                                m->mothurOut("Unable to open " + it->second + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-                                               ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                               ifstream in2;
+                                               ableToOpen = m->openInputFile(tryPath, in2, "noerror");
                                                container[parameter] = tryPath;
+                                               in2.close();
                                        }
                                }
                                
-                               in.close();
+                               
 
                        #ifdef USE_MPI  
                                        for(int i = 1; i < processors; i++) {